Starting phenix.real_space_refine on Thu Jul 2 04:46:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl1_40571/07_2026/8sl1_40571_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl1_40571/07_2026/8sl1_40571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_2026/8sl1_40571_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_2026/8sl1_40571_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_2026/8sl1_40571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_2026/8sl1_40571.map" } resolution = 3.13 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= 0.002 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 45 5.16 5 C 4157 2.51 5 N 1118 2.21 5 O 1285 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: 6608 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6562 Classifications: {'peptide': 843} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 64, 'TRANS': 778} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 16 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.44, per 1000 atoms: 0.22 Number of scatterers: 6608 At special positions: 0 Unit cell: (78.942, 86.301, 107.709, 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) Zn 1 29.99 Ca 2 19.99 S 45 16.00 O 1285 8.00 N 1118 7.00 C 4157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 580 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 769 " distance=2.04 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A 881 " - pdb=" SG CYS A 909 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 917 " distance=2.05 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1802 " - " ASN A 445 " " NAG B 1 " - " ASN A 328 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 350.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 499 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 509 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 503 " 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 17.4% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 163 through 168 removed outlier: 4.612A pdb=" N SER A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 removed outlier: 4.228A pdb=" N PHE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.259A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 268 through 271 Processing helix chain 'A' and resid 272 through 282 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 309 through 326 removed outlier: 3.541A pdb=" N ILE A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.679A pdb=" N ARG A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.579A pdb=" N GLU A 367 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.703A pdb=" N GLY A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.781A pdb=" N ILE A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.715A pdb=" N VAL A 746 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A 747 " --> pdb=" O SER A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 743 through 747' Processing helix chain 'A' and resid 808 through 812 Processing helix chain 'A' and resid 827 through 831 removed outlier: 4.042A pdb=" N LEU A 831 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 154 removed outlier: 5.362A pdb=" N GLN A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 146 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 138 " --> pdb=" O HIS A 141 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 54 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 194 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A 56 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 192 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP A 58 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 192 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 5.362A pdb=" N GLN A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 146 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 138 " --> pdb=" O HIS A 141 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 54 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 194 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A 56 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 192 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP A 58 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR A 191 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.598A pdb=" N ILE A 91 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE A 70 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 172 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 337 removed outlier: 6.420A pdb=" N LYS A 289 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLN A 332 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 291 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER A 334 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N HIS A 336 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 295 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N LEU A 450 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG A 292 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE A 452 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A 294 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA6, first strand: chain 'A' and resid 617 through 621 removed outlier: 6.886A pdb=" N THR A 627 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 657 through 659 removed outlier: 6.671A pdb=" N ILE A 797 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 736 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 799 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU A 734 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 801 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 732 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A 803 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 717 through 727 removed outlier: 6.070A pdb=" N SER A 784 " --> pdb=" O PHE A 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 833 through 835 185 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2180 1.34 - 1.46: 1500 1.46 - 1.58: 3047 1.58 - 1.70: 0 1.70 - 1.83: 59 Bond restraints: 6786 Sorted by residual: bond pdb=" N ASP A 883 " pdb=" CA ASP A 883 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.40e-02 5.10e+03 7.21e+00 bond pdb=" N GLU A 893 " pdb=" CA GLU A 893 " ideal model delta sigma weight residual 1.461 1.487 -0.026 9.70e-03 1.06e+04 6.98e+00 bond pdb=" N TYR A 925 " pdb=" CA TYR A 925 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.59e+00 bond pdb=" N GLN A 205 " pdb=" CA GLN A 205 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.46e+00 bond pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.46e+00 ... (remaining 6781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8967 1.53 - 3.06: 228 3.06 - 4.60: 58 4.60 - 6.13: 3 6.13 - 7.66: 2 Bond angle restraints: 9258 Sorted by residual: angle pdb=" C CYS A 894 " pdb=" CA CYS A 894 " pdb=" CB CYS A 894 " ideal model delta sigma weight residual 111.31 103.65 7.66 1.68e+00 3.54e-01 2.08e+01 angle pdb=" N PRO A 871 " pdb=" CA PRO A 871 " pdb=" C PRO A 871 " ideal model delta sigma weight residual 110.55 117.44 -6.89 1.63e+00 3.76e-01 1.78e+01 angle pdb=" CA ASP A 895 " pdb=" C ASP A 895 " pdb=" O ASP A 895 " ideal model delta sigma weight residual 122.37 117.90 4.47 1.15e+00 7.56e-01 1.51e+01 angle pdb=" C CYS A 917 " pdb=" CA CYS A 917 " pdb=" CB CYS A 917 " ideal model delta sigma weight residual 109.84 115.15 -5.31 1.50e+00 4.44e-01 1.25e+01 angle pdb=" N ILE A 71 " pdb=" CA ILE A 71 " pdb=" C ILE A 71 " ideal model delta sigma weight residual 111.58 108.31 3.27 1.06e+00 8.90e-01 9.54e+00 ... (remaining 9253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3568 17.99 - 35.99: 405 35.99 - 53.98: 99 53.98 - 71.98: 26 71.98 - 89.97: 8 Dihedral angle restraints: 4106 sinusoidal: 1674 harmonic: 2432 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -41.99 -44.01 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA GLU A 227 " pdb=" C GLU A 227 " pdb=" N PRO A 228 " pdb=" CA PRO A 228 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 366 " pdb=" CB CYS A 366 " ideal model delta sinusoidal sigma weight residual 93.00 125.62 -32.62 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 4103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1016 0.261 - 0.522: 1 0.522 - 0.782: 1 0.782 - 1.043: 0 1.043 - 1.304: 1 Chirality restraints: 1019 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.05e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" C1 NAG A1802 " pdb=" ND2 ASN A 445 " pdb=" C2 NAG A1802 " pdb=" O5 NAG A1802 " both_signs ideal model delta sigma weight residual False -2.40 -2.90 0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 1016 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 328 " 0.164 2.00e-02 2.50e+03 1.96e-01 4.80e+02 pdb=" CG ASN A 328 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 328 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 328 " -0.322 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 445 " 0.035 2.00e-02 2.50e+03 3.66e-02 1.67e+01 pdb=" CG ASN A 445 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 445 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 445 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG A1802 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 591 " 0.215 9.50e-02 1.11e+02 9.65e-02 5.73e+00 pdb=" NE ARG A 591 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 591 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 591 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 591 " 0.008 2.00e-02 2.50e+03 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 976 2.76 - 3.29: 6404 3.29 - 3.83: 10704 3.83 - 4.36: 13155 4.36 - 4.90: 22692 Nonbonded interactions: 53931 Sorted by model distance: nonbonded pdb=" O ALA A 828 " pdb=" OG SER A 829 " model vdw 2.223 3.040 nonbonded pdb=" O GLY A 64 " pdb=" NH1 ARG A 186 " model vdw 2.243 3.120 nonbonded pdb=" O TYR A 880 " pdb="CA CA A1804 " model vdw 2.262 3.250 nonbonded pdb=" OD1 ASP A 792 " pdb=" N ILE A 795 " model vdw 2.297 3.120 nonbonded pdb=" O CYS A 524 " pdb=" N GLY A 534 " model vdw 2.309 3.120 ... (remaining 53926 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.007 0.280 6803 Z= 0.273 Angle : 0.743 23.007 9289 Z= 0.378 Chirality : 0.065 1.304 1019 Planarity : 0.005 0.096 1217 Dihedral : 16.399 89.971 2509 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.68 % Allowed : 17.71 % Favored : 81.61 % 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: -0.41 (0.30), residues: 835 helix: 0.32 (0.62), residues: 76 sheet: -0.82 (0.38), residues: 184 loop : -0.09 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 591 TYR 0.009 0.001 TYR A 282 PHE 0.006 0.001 PHE A 511 TRP 0.008 0.001 TRP A 283 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 ( 6786) covalent geometry : angle 0.60869 / 0.35 ( 9258) SS BOND : bond 0.00623 / 0.28 ( 11) SS BOND : angle 1.41653 / 0.59 ( 22) hydrogen bonds : bond 0.15648 / 10.62 ( 166) hydrogen bonds : angle 6.59717 / 4.66 ( 453) metal coordination : bond 0.27895 / 15.69 ( 3) link_BETA1-4 : bond 0.00201 / 0.13 ( 1) link_BETA1-4 : angle 16.22555 / 7.36 ( 3) link_NAG-ASN : bond 0.00820 / 0.47 ( 2) link_NAG-ASN : angle 11.98337 / 8.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.4578 (ppp) cc_final: 0.4201 (ppp) REVERT: A 573 MET cc_start: 0.7922 (mmm) cc_final: 0.7662 (mmm) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.0871 time to fit residues: 8.3421 Evaluate side-chains 67 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4339 r_free = 0.4339 target = 0.187326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140922 restraints weight = 7082.299| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.84 r_work: 0.3667 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6803 Z= 0.175 Angle : 0.626 11.678 9289 Z= 0.308 Chirality : 0.044 0.145 1019 Planarity : 0.005 0.053 1217 Dihedral : 5.548 58.548 972 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.86 % Allowed : 16.62 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.30), residues: 835 helix: 0.51 (0.59), residues: 75 sheet: -0.84 (0.39), residues: 178 loop : -0.11 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 103 TYR 0.009 0.001 TYR A 293 PHE 0.016 0.002 PHE A 511 TRP 0.008 0.001 TRP A 468 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 ( 6786) covalent geometry : angle 0.62012 / 0.31 ( 9258) SS BOND : bond 0.00302 / 0.16 ( 11) SS BOND : angle 0.95753 / 0.54 ( 22) hydrogen bonds : bond 0.03750 / 2.48 ( 166) hydrogen bonds : angle 5.51698 / 3.87 ( 453) metal coordination : bond 0.00821 / 0.50 ( 3) link_BETA1-4 : bond 0.00233 / 0.15 ( 1) link_BETA1-4 : angle 2.49318 / 1.03 ( 3) link_NAG-ASN : bond 0.00366 / 0.23 ( 2) link_NAG-ASN : angle 2.71411 / 1.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 140 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.8072 (mtm-85) REVERT: A 166 MET cc_start: 0.5142 (ppp) cc_final: 0.4579 (ppp) outliers start: 21 outliers final: 11 residues processed: 92 average time/residue: 0.0687 time to fit residues: 8.6713 Evaluate side-chains 77 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 44 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.188160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141937 restraints weight = 7010.625| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.83 r_work: 0.3682 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6803 Z= 0.137 Angle : 0.579 12.111 9289 Z= 0.284 Chirality : 0.043 0.145 1019 Planarity : 0.005 0.052 1217 Dihedral : 5.274 57.257 970 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.72 % Allowed : 18.12 % Favored : 79.16 % 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 (0.30), residues: 835 helix: 0.79 (0.59), residues: 75 sheet: -0.83 (0.39), residues: 184 loop : 0.00 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.020 0.001 TYR A 880 PHE 0.014 0.001 PHE A 511 TRP 0.008 0.001 TRP A 468 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6786) covalent geometry : angle 0.57452 / 0.28 ( 9258) SS BOND : bond 0.00216 / 0.13 ( 11) SS BOND : angle 0.71293 / 0.42 ( 22) hydrogen bonds : bond 0.03122 / 2.02 ( 166) hydrogen bonds : angle 5.35731 / 3.75 ( 453) metal coordination : bond 0.00261 / 0.15 ( 3) link_BETA1-4 : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : angle 2.28679 / 0.93 ( 3) link_NAG-ASN : bond 0.00118 / 0.07 ( 2) link_NAG-ASN : angle 2.44078 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.6995 (Cg_endo) cc_final: 0.6605 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7538 (mp) REVERT: A 140 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.8035 (mtm-85) REVERT: A 144 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7458 (tp) REVERT: A 272 ASN cc_start: 0.6093 (t0) cc_final: 0.5858 (m-40) REVERT: A 345 HIS cc_start: 0.7297 (m-70) cc_final: 0.7069 (m90) outliers start: 20 outliers final: 13 residues processed: 89 average time/residue: 0.0666 time to fit residues: 8.2489 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4357 r_free = 0.4357 target = 0.189348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143138 restraints weight = 7049.149| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.85 r_work: 0.3691 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6803 Z= 0.120 Angle : 0.556 12.303 9289 Z= 0.270 Chirality : 0.042 0.140 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.942 53.175 968 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.54 % Allowed : 18.80 % Favored : 77.66 % 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 (0.30), residues: 835 helix: 0.92 (0.59), residues: 76 sheet: -0.77 (0.38), residues: 185 loop : 0.08 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.009 0.001 TYR A 880 PHE 0.014 0.001 PHE A 511 TRP 0.007 0.001 TRP A 468 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 6786) covalent geometry : angle 0.55215 / 0.27 ( 9258) SS BOND : bond 0.00167 / 0.10 ( 11) SS BOND : angle 0.60081 / 0.35 ( 22) hydrogen bonds : bond 0.02865 / 1.86 ( 166) hydrogen bonds : angle 5.21515 / 3.66 ( 453) metal coordination : bond 0.00147 / 0.08 ( 3) link_BETA1-4 : bond 0.00154 / 0.10 ( 1) link_BETA1-4 : angle 2.10097 / 0.90 ( 3) link_NAG-ASN : bond 0.00086 / 0.05 ( 2) link_NAG-ASN : angle 2.20360 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7015 (Cg_endo) cc_final: 0.6673 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7577 (mp) REVERT: A 276 ILE cc_start: 0.5575 (OUTLIER) cc_final: 0.5332 (tp) REVERT: A 664 SER cc_start: 0.8204 (t) cc_final: 0.7612 (m) outliers start: 26 outliers final: 16 residues processed: 93 average time/residue: 0.0692 time to fit residues: 9.0051 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4362 r_free = 0.4362 target = 0.189880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143209 restraints weight = 7100.979| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.86 r_work: 0.3696 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6803 Z= 0.117 Angle : 0.543 12.168 9289 Z= 0.265 Chirality : 0.042 0.136 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.825 50.925 968 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.27 % Allowed : 19.62 % Favored : 77.11 % 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 (0.30), residues: 835 helix: 1.01 (0.61), residues: 75 sheet: -0.73 (0.38), residues: 185 loop : 0.13 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.008 0.001 TYR A 595 PHE 0.013 0.001 PHE A 511 TRP 0.007 0.001 TRP A 468 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6786) covalent geometry : angle 0.53888 / 0.26 ( 9258) SS BOND : bond 0.00154 / 0.08 ( 11) SS BOND : angle 0.54350 / 0.32 ( 22) hydrogen bonds : bond 0.02769 / 1.80 ( 166) hydrogen bonds : angle 5.15951 / 3.62 ( 453) metal coordination : bond 0.00138 / 0.08 ( 3) link_BETA1-4 : bond 0.00033 / 0.02 ( 1) link_BETA1-4 : angle 2.09852 / 0.88 ( 3) link_NAG-ASN : bond 0.00116 / 0.07 ( 2) link_NAG-ASN : angle 2.17369 / 1.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7067 (Cg_endo) cc_final: 0.6780 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 275 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6395 (tp) REVERT: A 345 HIS cc_start: 0.7314 (m-70) cc_final: 0.7097 (m90) REVERT: A 664 SER cc_start: 0.8203 (t) cc_final: 0.7616 (m) outliers start: 24 outliers final: 19 residues processed: 89 average time/residue: 0.0717 time to fit residues: 8.9039 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4377 r_free = 0.4377 target = 0.191249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144891 restraints weight = 7005.081| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.83 r_work: 0.3703 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6803 Z= 0.101 Angle : 0.534 11.777 9289 Z= 0.260 Chirality : 0.042 0.150 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.660 48.175 968 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.86 % Allowed : 20.44 % Favored : 76.70 % 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: 0.06 (0.31), residues: 835 helix: 1.33 (0.65), residues: 69 sheet: -0.65 (0.38), residues: 185 loop : 0.22 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 344 TYR 0.008 0.001 TYR A 145 PHE 0.013 0.001 PHE A 511 TRP 0.007 0.001 TRP A 470 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 ( 6786) covalent geometry : angle 0.53086 / 0.26 ( 9258) SS BOND : bond 0.00115 / 0.07 ( 11) SS BOND : angle 0.45238 / 0.29 ( 22) hydrogen bonds : bond 0.02672 / 1.74 ( 166) hydrogen bonds : angle 5.01711 / 3.52 ( 453) metal coordination : bond 0.00170 / 0.10 ( 3) link_BETA1-4 : bond 0.00147 / 0.09 ( 1) link_BETA1-4 : angle 2.01558 / 0.88 ( 3) link_NAG-ASN : bond 0.00110 / 0.07 ( 2) link_NAG-ASN : angle 2.06298 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7006 (Cg_endo) cc_final: 0.6750 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 318 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6623 (mt-10) REVERT: A 664 SER cc_start: 0.8168 (t) cc_final: 0.7579 (m) outliers start: 21 outliers final: 15 residues processed: 88 average time/residue: 0.0651 time to fit residues: 8.1624 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.0060 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 33 optimal weight: 0.0270 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.193275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147045 restraints weight = 6936.601| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.84 r_work: 0.3730 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6803 Z= 0.091 Angle : 0.522 11.492 9289 Z= 0.254 Chirality : 0.041 0.149 1019 Planarity : 0.004 0.049 1217 Dihedral : 4.435 45.438 968 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.00 % Allowed : 20.44 % Favored : 76.57 % 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 (0.31), residues: 835 helix: 1.50 (0.66), residues: 69 sheet: -0.54 (0.39), residues: 186 loop : 0.28 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.008 0.001 TYR A 145 PHE 0.030 0.001 PHE A 740 TRP 0.008 0.001 TRP A 283 HIS 0.010 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.09 ( 6786) covalent geometry : angle 0.51861 / 0.25 ( 9258) SS BOND : bond 0.00129 / 0.09 ( 11) SS BOND : angle 0.39845 / 0.28 ( 22) hydrogen bonds : bond 0.02447 / 1.59 ( 166) hydrogen bonds : angle 4.80311 / 3.37 ( 453) metal coordination : bond 0.00074 / 0.04 ( 3) link_BETA1-4 : bond 0.00078 / 0.05 ( 1) link_BETA1-4 : angle 1.90121 / 0.84 ( 3) link_NAG-ASN : bond 0.00097 / 0.06 ( 2) link_NAG-ASN : angle 1.96961 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.6958 (Cg_endo) cc_final: 0.6711 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7454 (mp) REVERT: A 240 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7507 (ttpt) REVERT: A 318 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6748 (mm-30) REVERT: A 345 HIS cc_start: 0.7267 (m-70) cc_final: 0.7034 (m90) REVERT: A 664 SER cc_start: 0.8145 (t) cc_final: 0.7565 (m) REVERT: A 917 CYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6729 (p) outliers start: 22 outliers final: 19 residues processed: 89 average time/residue: 0.0767 time to fit residues: 9.5720 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 55 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4429 r_free = 0.4429 target = 0.195236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153296 restraints weight = 6925.182| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.86 r_work: 0.3783 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6803 Z= 0.095 Angle : 0.519 11.461 9289 Z= 0.254 Chirality : 0.041 0.145 1019 Planarity : 0.005 0.081 1217 Dihedral : 4.401 44.480 968 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.27 % Allowed : 20.03 % Favored : 76.70 % 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: 0.25 (0.31), residues: 835 helix: 1.54 (0.66), residues: 69 sheet: -0.45 (0.39), residues: 186 loop : 0.32 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.007 0.001 TYR A 145 PHE 0.014 0.001 PHE A 748 TRP 0.007 0.001 TRP A 470 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.09 ( 6786) covalent geometry : angle 0.51561 / 0.25 ( 9258) SS BOND : bond 0.00100 / 0.06 ( 11) SS BOND : angle 0.38907 / 0.25 ( 22) hydrogen bonds : bond 0.02496 / 1.63 ( 166) hydrogen bonds : angle 4.71658 / 3.30 ( 453) metal coordination : bond 0.00084 / 0.05 ( 3) link_BETA1-4 : bond 0.00175 / 0.11 ( 1) link_BETA1-4 : angle 1.87325 / 0.84 ( 3) link_NAG-ASN : bond 0.00090 / 0.05 ( 2) link_NAG-ASN : angle 2.03159 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.6989 (Cg_endo) cc_final: 0.6763 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 166 MET cc_start: 0.5147 (ppp) cc_final: 0.4688 (ppp) REVERT: A 318 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6762 (mm-30) REVERT: A 345 HIS cc_start: 0.7248 (m-70) cc_final: 0.7017 (m90) REVERT: A 664 SER cc_start: 0.8087 (t) cc_final: 0.7564 (m) REVERT: A 917 CYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6745 (p) outliers start: 24 outliers final: 19 residues processed: 91 average time/residue: 0.0680 time to fit residues: 8.8103 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4336 r_free = 0.4336 target = 0.187183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139885 restraints weight = 7196.555| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.91 r_work: 0.3669 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6803 Z= 0.198 Angle : 0.625 12.815 9289 Z= 0.305 Chirality : 0.045 0.153 1019 Planarity : 0.006 0.088 1217 Dihedral : 5.021 49.558 968 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.27 % Allowed : 19.89 % Favored : 76.84 % 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 (0.30), residues: 835 helix: 0.98 (0.63), residues: 69 sheet: -0.72 (0.39), residues: 173 loop : 0.12 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.013 0.001 TYR A 595 PHE 0.032 0.002 PHE A 740 TRP 0.007 0.002 TRP A 630 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 6786) covalent geometry : angle 0.62054 / 0.30 ( 9258) SS BOND : bond 0.00321 / 0.17 ( 11) SS BOND : angle 0.54627 / 0.36 ( 22) hydrogen bonds : bond 0.03268 / 2.13 ( 166) hydrogen bonds : angle 5.17875 / 3.62 ( 453) metal coordination : bond 0.00340 / 0.19 ( 3) link_BETA1-4 : bond 0.00250 / 0.16 ( 1) link_BETA1-4 : angle 2.19726 / 0.93 ( 3) link_NAG-ASN : bond 0.00304 / 0.18 ( 2) link_NAG-ASN : angle 2.52819 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7139 (Cg_endo) cc_final: 0.6868 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 166 MET cc_start: 0.5015 (ppp) cc_final: 0.4517 (ppp) REVERT: A 318 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6829 (mm-30) REVERT: A 345 HIS cc_start: 0.7373 (m-70) cc_final: 0.7165 (m90) outliers start: 24 outliers final: 20 residues processed: 87 average time/residue: 0.0700 time to fit residues: 8.5583 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 76 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4405 r_free = 0.4405 target = 0.191732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.149045 restraints weight = 6864.724| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.89 r_work: 0.3739 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6803 Z= 0.103 Angle : 0.540 12.219 9289 Z= 0.265 Chirality : 0.042 0.144 1019 Planarity : 0.005 0.081 1217 Dihedral : 4.579 44.072 968 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.45 % Allowed : 20.44 % Favored : 77.11 % 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: 0.19 (0.31), residues: 835 helix: 1.24 (0.65), residues: 69 sheet: -0.49 (0.38), residues: 185 loop : 0.30 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.008 0.001 TYR A 789 PHE 0.030 0.001 PHE A 740 TRP 0.010 0.001 TRP A 283 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.10 ( 6786) covalent geometry : angle 0.53718 / 0.26 ( 9258) SS BOND : bond 0.00086 / 0.05 ( 11) SS BOND : angle 0.43366 / 0.30 ( 22) hydrogen bonds : bond 0.02613 / 1.70 ( 166) hydrogen bonds : angle 4.86367 / 3.40 ( 453) metal coordination : bond 0.00118 / 0.07 ( 3) link_BETA1-4 : bond 0.00223 / 0.14 ( 1) link_BETA1-4 : angle 1.98186 / 0.89 ( 3) link_NAG-ASN : bond 0.00102 / 0.06 ( 2) link_NAG-ASN : angle 1.93003 / 1.16 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.244 Fit side-chains REVERT: A 68 PRO cc_start: 0.7085 (Cg_endo) cc_final: 0.6835 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7447 (mp) REVERT: A 166 MET cc_start: 0.5011 (ppp) cc_final: 0.4566 (ppp) REVERT: A 318 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 345 HIS cc_start: 0.7342 (m-70) cc_final: 0.7132 (m90) REVERT: A 664 SER cc_start: 0.8142 (t) cc_final: 0.7581 (m) REVERT: A 917 CYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6882 (p) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.0676 time to fit residues: 8.5144 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 593 HIS ** 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 = 0.4398 r_free = 0.4398 target = 0.190625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150119 restraints weight = 6805.248| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.72 r_work: 0.3746 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6803 Z= 0.117 Angle : 0.544 12.155 9289 Z= 0.265 Chirality : 0.042 0.146 1019 Planarity : 0.005 0.085 1217 Dihedral : 4.619 44.748 968 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.45 % Allowed : 20.57 % Favored : 76.98 % 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: 0.23 (0.31), residues: 835 helix: 1.28 (0.65), residues: 69 sheet: -0.50 (0.39), residues: 180 loop : 0.34 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.009 0.001 TYR A 595 PHE 0.013 0.001 PHE A 748 TRP 0.006 0.001 TRP A 468 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 6786) covalent geometry : angle 0.54011 / 0.26 ( 9258) SS BOND : bond 0.00134 / 0.08 ( 11) SS BOND : angle 0.39718 / 0.28 ( 22) hydrogen bonds : bond 0.02690 / 1.74 ( 166) hydrogen bonds : angle 4.85671 / 3.40 ( 453) metal coordination : bond 0.00144 / 0.08 ( 3) link_BETA1-4 : bond 0.00116 / 0.07 ( 1) link_BETA1-4 : angle 1.98732 / 0.86 ( 3) link_NAG-ASN : bond 0.00124 / 0.08 ( 2) link_NAG-ASN : angle 2.18418 / 1.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.72 seconds wall clock time: 27 minutes 55.21 seconds (1675.21 seconds total)