Starting phenix.real_space_refine on Thu Nov 14 16:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl1_40571/11_2024/8sl1_40571_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl1_40571/11_2024/8sl1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl1_40571/11_2024/8sl1_40571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl1_40571/11_2024/8sl1_40571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl1_40571/11_2024/8sl1_40571_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sl1_40571/11_2024/8sl1_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-5513/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: 5.10, per 1000 atoms: 0.77 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.80 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: 2.37 Time building geometry restraints manager: 1.92 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: 2.640 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.780 Find NCS groups from input model: 0.070 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- 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 : 0.724 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: 0.2507 time to fit residues: 23.6212 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 : 0.786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.0894 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= 0.201 Angle : 0.572 10.760 9258 Z= 0.283 Chirality : 0.042 0.134 1019 Planarity : 0.005 0.057 1217 Dihedral : 5.344 59.150 972 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 16.62 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (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 0.000 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 : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 166 MET cc_start: 0.5010 (ppp) cc_final: 0.4617 (ppp) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 0.1897 time to fit residues: 23.1481 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 : 0.799 ------------------------------------------------------------------------------- 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 42 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6786 Z= 0.223 Angle : 0.562 11.533 9258 Z= 0.276 Chirality : 0.043 0.142 1019 Planarity : 0.005 0.049 1217 Dihedral : 5.103 57.920 969 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.59 % Allowed : 17.71 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.31), residues: 835 helix: 0.98 (0.60), residues: 75 sheet: -0.69 (0.39), residues: 185 loop : 0.10 (0.28), residues: 575 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7241 (Cg_endo) cc_final: 0.6840 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7748 (mp) outliers start: 19 outliers final: 12 residues processed: 90 average time/residue: 0.1879 time to fit residues: 23.0194 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6786 Z= 0.169 Angle : 0.532 11.760 9258 Z= 0.260 Chirality : 0.042 0.138 1019 Planarity : 0.005 0.047 1217 Dihedral : 4.760 52.788 968 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.27 % Allowed : 17.57 % 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 (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: 0.07 (0.31), residues: 835 helix: 1.08 (0.61), residues: 76 sheet: -0.60 (0.38), residues: 185 loop : 0.23 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.009 0.001 HIS A 345 PHE 0.018 0.001 PHE A 740 TYR 0.013 0.001 TYR A 880 ARG 0.002 0.000 ARG A 346 *********************** 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 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7218 (Cg_endo) cc_final: 0.6900 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 240 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7522 (ttpt) REVERT: A 664 SER cc_start: 0.8054 (t) cc_final: 0.7565 (m) outliers start: 24 outliers final: 14 residues processed: 95 average time/residue: 0.1755 time to fit residues: 23.2127 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 276 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 6786 Z= 0.491 Angle : 0.725 13.724 9258 Z= 0.356 Chirality : 0.048 0.154 1019 Planarity : 0.006 0.058 1217 Dihedral : 5.759 57.810 968 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.54 % Allowed : 19.07 % Favored : 77.38 % 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: -0.55 (0.30), residues: 835 helix: 0.27 (0.57), residues: 75 sheet: -1.15 (0.37), residues: 187 loop : -0.09 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 630 HIS 0.010 0.002 HIS A 345 PHE 0.022 0.003 PHE A 31 TYR 0.015 0.002 TYR A 595 ARG 0.004 0.001 ARG A 41 *********************** 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 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7555 (Cg_endo) cc_final: 0.7144 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7800 (mp) REVERT: A 275 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6665 (tp) outliers start: 26 outliers final: 17 residues processed: 94 average time/residue: 0.1873 time to fit residues: 23.9009 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 514 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 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 27 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6786 Z= 0.219 Angle : 0.583 13.543 9258 Z= 0.286 Chirality : 0.043 0.140 1019 Planarity : 0.005 0.053 1217 Dihedral : 5.172 50.816 968 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.00 % Allowed : 19.62 % Favored : 77.38 % 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: 0.47 (0.57), residues: 75 sheet: -1.02 (0.37), residues: 195 loop : 0.08 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.007 0.001 HIS A 499 PHE 0.013 0.001 PHE A 511 TYR 0.009 0.001 TYR A 880 ARG 0.003 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7466 (Cg_endo) cc_final: 0.7099 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 318 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6668 (mt-10) outliers start: 22 outliers final: 16 residues processed: 87 average time/residue: 0.1689 time to fit residues: 20.4423 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 : 0.661 ------------------------------------------------------------------------------- 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 272 ASN 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 730 ASP 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 78 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6786 Z= 0.310 Angle : 0.618 13.560 9258 Z= 0.303 Chirality : 0.044 0.145 1019 Planarity : 0.005 0.053 1217 Dihedral : 5.280 51.461 968 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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 (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: -0.44 (0.30), residues: 835 helix: 0.33 (0.57), residues: 75 sheet: -1.10 (0.36), residues: 195 loop : 0.02 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 468 HIS 0.010 0.001 HIS A 345 PHE 0.014 0.002 PHE A 31 TYR 0.009 0.001 TYR A 595 ARG 0.003 0.000 ARG A 186 *********************** 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: 24 poor density : 70 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7516 (Cg_endo) cc_final: 0.7139 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7764 (mp) REVERT: A 318 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6671 (mt-10) outliers start: 24 outliers final: 18 residues processed: 88 average time/residue: 0.1761 time to fit residues: 21.9563 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 730 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 : 0.003 0.043 6786 Z= 0.218 Angle : 0.573 12.947 9258 Z= 0.281 Chirality : 0.043 0.140 1019 Planarity : 0.005 0.051 1217 Dihedral : 5.013 45.286 968 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.59 % Allowed : 20.71 % 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 (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: -0.27 (0.30), residues: 835 helix: 0.49 (0.58), residues: 75 sheet: -0.99 (0.37), residues: 195 loop : 0.14 (0.29), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.007 0.001 HIS A 499 PHE 0.013 0.001 PHE A 511 TYR 0.008 0.001 TYR A 789 ARG 0.003 0.000 ARG A 186 *********************** 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 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7441 (Cg_endo) cc_final: 0.7097 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 318 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6674 (mt-10) REVERT: A 917 CYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6532 (p) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.1927 time to fit residues: 21.5586 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 272 ASN 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 585 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 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 75 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.003 0.042 6786 Z= 0.202 Angle : 0.564 12.834 9258 Z= 0.276 Chirality : 0.042 0.141 1019 Planarity : 0.005 0.055 1217 Dihedral : 4.929 44.294 968 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.00 % Allowed : 20.16 % 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 (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: -0.15 (0.31), residues: 835 helix: 0.82 (0.62), residues: 69 sheet: -0.93 (0.37), residues: 195 loop : 0.20 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 468 HIS 0.008 0.001 HIS A 345 PHE 0.012 0.001 PHE A 511 TYR 0.009 0.001 TYR A 595 ARG 0.003 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 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7405 (Cg_endo) cc_final: 0.7092 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 318 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6666 (mt-10) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.1676 time to fit residues: 20.0233 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 501 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 585 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 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 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6786 Z= 0.181 Angle : 0.553 12.584 9258 Z= 0.272 Chirality : 0.042 0.140 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.571 21.243 967 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.72 % Allowed : 20.44 % 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 (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: 0.92 (0.63), residues: 70 sheet: -0.77 (0.38), residues: 185 loop : 0.24 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.007 0.001 HIS A 499 PHE 0.012 0.001 PHE A 511 TYR 0.008 0.001 TYR A 595 ARG 0.003 0.000 ARG A 186 ********************** 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 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7388 (Cg_endo) cc_final: 0.7107 (Cg_exo) REVERT: A 70 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 275 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6493 (tp) REVERT: A 318 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6647 (mt-10) outliers start: 20 outliers final: 16 residues processed: 85 average time/residue: 0.1766 time to fit residues: 21.1923 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 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 924 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 0.0020 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.190299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146645 restraints weight = 6920.871| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.96 r_work: 0.3718 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6786 Z= 0.185 Angle : 0.551 12.429 9258 Z= 0.271 Chirality : 0.042 0.141 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.490 20.125 967 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.45 % Allowed : 20.98 % 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: 0.08 (0.31), residues: 835 helix: 1.00 (0.63), residues: 70 sheet: -0.71 (0.38), residues: 185 loop : 0.31 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 283 HIS 0.009 0.001 HIS A 345 PHE 0.011 0.001 PHE A 511 TYR 0.008 0.001 TYR A 595 ARG 0.003 0.000 ARG A 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.21 seconds wall clock time: 32 minutes 43.11 seconds (1963.11 seconds total)