Starting phenix.real_space_refine on Tue Mar 11 21:58:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl1_40571/03_2025/8sl1_40571_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl1_40571/03_2025/8sl1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sl1_40571/03_2025/8sl1_40571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl1_40571/03_2025/8sl1_40571.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl1_40571/03_2025/8sl1_40571_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl1_40571/03_2025/8sl1_40571_neut.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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, 18 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.03, per 1000 atoms: 0.76 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: 1.68 Conformation dependent library (CDL) restraints added in 950.5 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: 0.85 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: 2.13 Time building geometry restraints manager: 2.01 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 2.510 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: 3.380 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.003 0.038 6786 Z= 0.215 Angle : 0.609 7.659 9258 Z= 0.350 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 283 HIS 0.005 0.001 HIS A 499 PHE 0.006 0.001 PHE A 511 TYR 0.009 0.001 TYR A 282 ARG 0.002 0.000 ARG A 591 *********************** 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 : 0.649 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: 0.2280 time to fit residues: 21.5734 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 : 0.651 ------------------------------------------------------------------------------- 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 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4365 r_free = 0.4365 target = 0.190036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144643 restraints weight = 6928.903| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.79 r_work: 0.3716 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6786 Z= 0.200 Angle : 0.572 10.751 9258 Z= 0.283 Chirality : 0.042 0.134 1019 Planarity : 0.005 0.057 1217 Dihedral : 5.345 59.085 972 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 16.49 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 835 helix: 0.76 (0.60), residues: 76 sheet: -0.76 (0.38), residues: 185 loop : 0.08 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.009 0.001 HIS A 345 PHE 0.015 0.001 PHE A 511 TYR 0.008 0.001 TYR A 508 ARG 0.004 0.001 ARG A 103 *********************** 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 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 166 MET cc_start: 0.5157 (ppp) cc_final: 0.4613 (ppp) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 0.1880 time to fit residues: 22.9990 Evaluate side-chains 76 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4340 r_free = 0.4340 target = 0.187776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141447 restraints weight = 7046.944| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.82 r_work: 0.3674 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6786 Z= 0.259 Angle : 0.583 11.943 9258 Z= 0.287 Chirality : 0.043 0.142 1019 Planarity : 0.005 0.051 1217 Dihedral : 5.216 58.367 969 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.59 % Allowed : 17.85 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.30), residues: 835 helix: 0.85 (0.59), residues: 75 sheet: -0.72 (0.39), residues: 178 loop : 0.03 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 HIS 0.009 0.001 HIS A 345 PHE 0.021 0.002 PHE A 740 TYR 0.021 0.001 TYR A 880 ARG 0.003 0.000 ARG A 103 *********************** 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 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.6980 (Cg_endo) cc_final: 0.6583 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 140 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: A 272 ASN cc_start: 0.6120 (t0) cc_final: 0.5881 (m-40) REVERT: A 691 GLU cc_start: 0.6741 (tp30) cc_final: 0.6533 (mm-30) outliers start: 19 outliers final: 11 residues processed: 91 average time/residue: 0.1965 time to fit residues: 24.3793 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 730 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.184852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.138167 restraints weight = 7165.265| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.85 r_work: 0.3632 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6786 Z= 0.333 Angle : 0.629 13.246 9258 Z= 0.308 Chirality : 0.045 0.144 1019 Planarity : 0.005 0.054 1217 Dihedral : 5.381 55.830 968 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.54 % Allowed : 18.94 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 835 helix: 0.53 (0.58), residues: 75 sheet: -1.03 (0.37), residues: 187 loop : -0.04 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 468 HIS 0.010 0.001 HIS A 345 PHE 0.015 0.002 PHE A 31 TYR 0.013 0.002 TYR A 880 ARG 0.003 0.000 ARG A 186 *********************** 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6750 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7561 (mp) REVERT: A 140 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: A 144 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 275 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6550 (tp) REVERT: A 276 ILE cc_start: 0.5934 (OUTLIER) cc_final: 0.5702 (tp) REVERT: A 691 GLU cc_start: 0.6888 (tp30) cc_final: 0.6620 (mm-30) outliers start: 26 outliers final: 16 residues processed: 92 average time/residue: 0.1867 time to fit residues: 23.5567 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 199 LEU 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 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 47 optimal weight: 0.0370 chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141622 restraints weight = 7043.114| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.85 r_work: 0.3676 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6786 Z= 0.208 Angle : 0.564 12.895 9258 Z= 0.276 Chirality : 0.043 0.141 1019 Planarity : 0.005 0.051 1217 Dihedral : 5.038 51.353 968 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.41 % Allowed : 19.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.31), residues: 835 helix: 0.67 (0.58), residues: 75 sheet: -0.93 (0.37), residues: 195 loop : 0.10 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 468 HIS 0.007 0.001 HIS A 499 PHE 0.025 0.001 PHE A 740 TYR 0.011 0.001 TYR A 880 ARG 0.003 0.000 ARG A 186 *********************** 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7168 (Cg_endo) cc_final: 0.6825 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 140 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: A 144 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 691 GLU cc_start: 0.6883 (tp30) cc_final: 0.6661 (mm-30) outliers start: 25 outliers final: 16 residues processed: 90 average time/residue: 0.1728 time to fit residues: 21.7049 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 : 0.676 ------------------------------------------------------------------------------- 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 191 THR 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 604 THR Chi-restraints excluded: chain A residue 730 ASP 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 56 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.190804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145075 restraints weight = 6934.302| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.79 r_work: 0.3706 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6786 Z= 0.159 Angle : 0.527 12.225 9258 Z= 0.258 Chirality : 0.042 0.132 1019 Planarity : 0.005 0.049 1217 Dihedral : 4.718 47.664 968 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.86 % Allowed : 20.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 835 helix: 0.87 (0.60), residues: 75 sheet: -0.68 (0.38), residues: 185 loop : 0.20 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 283 HIS 0.011 0.001 HIS A 345 PHE 0.029 0.001 PHE A 740 TYR 0.009 0.001 TYR A 880 ARG 0.002 0.000 ARG A 186 *********************** 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7107 (Cg_endo) cc_final: 0.6827 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7524 (mp) REVERT: A 144 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7421 (tp) REVERT: A 318 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6656 (mt-10) REVERT: A 456 SER cc_start: 0.8344 (m) cc_final: 0.8079 (p) REVERT: A 664 SER cc_start: 0.8190 (t) cc_final: 0.7610 (m) REVERT: A 691 GLU cc_start: 0.6730 (tp30) cc_final: 0.6523 (mm-30) REVERT: A 917 CYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6734 (p) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.1716 time to fit residues: 22.1454 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 66 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4354 r_free = 0.4354 target = 0.189281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.142542 restraints weight = 6995.480| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.85 r_work: 0.3683 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6786 Z= 0.213 Angle : 0.555 12.117 9258 Z= 0.271 Chirality : 0.043 0.135 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.785 48.052 968 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.13 % Allowed : 20.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 835 helix: 0.82 (0.60), residues: 75 sheet: -0.66 (0.38), residues: 185 loop : 0.19 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 HIS 0.006 0.001 HIS A 499 PHE 0.012 0.001 PHE A 511 TYR 0.009 0.001 TYR A 595 ARG 0.007 0.000 ARG A 346 *********************** 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7119 (Cg_endo) cc_final: 0.6843 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7525 (mp) REVERT: A 318 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6676 (mt-10) REVERT: A 456 SER cc_start: 0.8335 (m) cc_final: 0.8076 (p) REVERT: A 691 GLU cc_start: 0.6756 (tp30) cc_final: 0.6552 (mm-30) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 0.1618 time to fit residues: 19.9439 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 604 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4352 r_free = 0.4352 target = 0.189104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142406 restraints weight = 6981.772| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.85 r_work: 0.3685 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6786 Z= 0.208 Angle : 0.550 12.060 9258 Z= 0.269 Chirality : 0.042 0.135 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.767 47.252 968 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.41 % Allowed : 20.30 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 835 helix: 0.85 (0.60), residues: 75 sheet: -0.66 (0.38), residues: 185 loop : 0.23 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 HIS 0.012 0.001 HIS A 345 PHE 0.013 0.001 PHE A 511 TYR 0.008 0.001 TYR A 595 ARG 0.005 0.000 ARG A 346 *********************** 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7078 (Cg_endo) cc_final: 0.6808 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7485 (mp) REVERT: A 318 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6754 (mm-30) REVERT: A 345 HIS cc_start: 0.7301 (m-70) cc_final: 0.7096 (m90) REVERT: A 456 SER cc_start: 0.8352 (m) cc_final: 0.8069 (p) REVERT: A 691 GLU cc_start: 0.6764 (tp30) cc_final: 0.6564 (mm-30) REVERT: A 917 CYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6778 (p) outliers start: 25 outliers final: 19 residues processed: 93 average time/residue: 0.1631 time to fit residues: 21.6364 Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 585 THR Chi-restraints excluded: chain A residue 604 THR 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 2 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.0370 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4347 r_free = 0.4347 target = 0.188343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144758 restraints weight = 6889.627| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.59 r_work: 0.3694 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6786 Z= 0.250 Angle : 0.574 12.455 9258 Z= 0.282 Chirality : 0.043 0.137 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.854 42.663 968 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.27 % Allowed : 20.57 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.30), residues: 835 helix: 0.77 (0.60), residues: 75 sheet: -0.68 (0.38), residues: 185 loop : 0.24 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 HIS 0.011 0.001 HIS A 345 PHE 0.014 0.001 PHE A 31 TYR 0.010 0.001 TYR A 595 ARG 0.004 0.000 ARG A 346 *********************** 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 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6848 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7502 (mp) REVERT: A 275 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6527 (tp) REVERT: A 318 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6691 (mt-10) REVERT: A 345 HIS cc_start: 0.7287 (m-70) cc_final: 0.7086 (m90) REVERT: A 456 SER cc_start: 0.8356 (m) cc_final: 0.8098 (p) outliers start: 24 outliers final: 19 residues processed: 90 average time/residue: 0.1668 time to fit residues: 21.4670 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 : 0.768 ------------------------------------------------------------------------------- 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 275 LEU 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 585 THR Chi-restraints excluded: chain A residue 604 THR 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 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 LEU 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 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4308 r_free = 0.4308 target = 0.184994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137920 restraints weight = 7193.018| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.83 r_work: 0.3640 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6786 Z= 0.352 Angle : 0.647 13.670 9258 Z= 0.318 Chirality : 0.046 0.157 1019 Planarity : 0.005 0.053 1217 Dihedral : 5.123 26.091 967 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.54 % Allowed : 20.44 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.30), residues: 835 helix: 0.34 (0.58), residues: 75 sheet: -0.96 (0.37), residues: 189 loop : 0.06 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 468 HIS 0.011 0.001 HIS A 345 PHE 0.017 0.002 PHE A 31 TYR 0.013 0.002 TYR A 595 ARG 0.004 0.001 ARG A 346 ********************** 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7257 (Cg_endo) cc_final: 0.6895 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 275 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6580 (tp) REVERT: A 318 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6739 (mt-10) REVERT: A 456 SER cc_start: 0.8383 (m) cc_final: 0.8088 (p) outliers start: 26 outliers final: 21 residues processed: 94 average time/residue: 0.1676 time to fit residues: 22.2057 Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 275 LEU 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 585 THR Chi-restraints excluded: chain A residue 604 THR 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 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 LEU 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 16 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4346 r_free = 0.4346 target = 0.188404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145038 restraints weight = 6999.065| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.58 r_work: 0.3681 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6786 Z= 0.235 Angle : 0.605 13.322 9258 Z= 0.297 Chirality : 0.043 0.139 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.896 24.084 967 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.00 % Allowed : 20.84 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 835 helix: 0.52 (0.58), residues: 75 sheet: -0.91 (0.36), residues: 194 loop : 0.15 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 468 HIS 0.006 0.001 HIS A 499 PHE 0.031 0.002 PHE A 740 TYR 0.009 0.001 TYR A 595 ARG 0.006 0.000 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3382.73 seconds wall clock time: 58 minutes 51.55 seconds (3531.55 seconds total)