Starting phenix.real_space_refine on Sat May 10 19:04:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl1_40571/05_2025/8sl1_40571_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl1_40571/05_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_40571/05_2025/8sl1_40571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl1_40571/05_2025/8sl1_40571.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl1_40571/05_2025/8sl1_40571_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl1_40571/05_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-5687/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: 5.14, per 1000 atoms: 0.78 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: 1.82 Conformation dependent library (CDL) restraints added in 953.8 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: 0.78 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: 2.27 Time building geometry restraints manager: 2.11 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: 3.340 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- 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 : 0.007 0.280 6803 Z= 0.273 Angle : 0.743 23.007 9289 Z= 0.378 Chirality : 0.065 1.304 1019 Planarity : 0.005 0.096 1217 Dihedral : 16.399 89.971 2509 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.68 % Allowed : 17.71 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 2) link_NAG-ASN : angle 11.98337 ( 6) link_BETA1-4 : bond 0.00201 ( 1) link_BETA1-4 : angle 16.22555 ( 3) hydrogen bonds : bond 0.15648 ( 166) hydrogen bonds : angle 6.59717 ( 453) metal coordination : bond 0.27895 ( 3) SS BOND : bond 0.00623 ( 11) SS BOND : angle 1.41653 ( 22) covalent geometry : bond 0.00324 ( 6786) covalent geometry : angle 0.60869 ( 9258) *********************** 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 : 0.675 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: 0.2295 time to fit residues: 21.6263 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 : 0.673 ------------------------------------------------------------------------------- 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: 0.8980 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: 3.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.189937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144526 restraints weight = 6929.469| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.78 r_work: 0.3715 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6803 Z= 0.124 Angle : 0.583 11.110 9289 Z= 0.287 Chirality : 0.043 0.150 1019 Planarity : 0.005 0.059 1217 Dihedral : 5.378 59.746 972 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.72 % Allowed : 16.76 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.31), residues: 835 helix: 0.75 (0.60), residues: 76 sheet: -0.77 (0.38), residues: 185 loop : 0.07 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 468 HIS 0.009 0.001 HIS A 345 PHE 0.016 0.001 PHE A 511 TYR 0.008 0.001 TYR A 508 ARG 0.005 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 2) link_NAG-ASN : angle 2.76553 ( 6) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 2.38445 ( 3) hydrogen bonds : bond 0.03221 ( 166) hydrogen bonds : angle 5.30303 ( 453) metal coordination : bond 0.00620 ( 3) SS BOND : bond 0.00227 ( 11) SS BOND : angle 0.83437 ( 22) covalent geometry : bond 0.00302 ( 6786) covalent geometry : angle 0.57679 ( 9258) *********************** 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 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 166 MET cc_start: 0.5150 (ppp) cc_final: 0.4613 (ppp) outliers start: 20 outliers final: 11 residues processed: 92 average time/residue: 0.1847 time to fit residues: 23.0185 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 475 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 70 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 = 0.189120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142851 restraints weight = 7009.699| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.82 r_work: 0.3688 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6803 Z= 0.139 Angle : 0.570 11.524 9289 Z= 0.279 Chirality : 0.043 0.141 1019 Planarity : 0.005 0.049 1217 Dihedral : 5.124 57.893 969 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.45 % Allowed : 18.12 % Favored : 79.43 % 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: -0.14 (0.31), residues: 835 helix: 0.94 (0.60), residues: 75 sheet: -0.75 (0.38), residues: 185 loop : 0.08 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 HIS 0.010 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 2) link_NAG-ASN : angle 2.47408 ( 6) link_BETA1-4 : bond 0.00167 ( 1) link_BETA1-4 : angle 2.25600 ( 3) hydrogen bonds : bond 0.03063 ( 166) hydrogen bonds : angle 5.28407 ( 453) metal coordination : bond 0.00319 ( 3) SS BOND : bond 0.00191 ( 11) SS BOND : angle 0.73697 ( 22) covalent geometry : bond 0.00343 ( 6786) covalent geometry : angle 0.56445 ( 9258) *********************** 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 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.6921 (Cg_endo) cc_final: 0.6524 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 140 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: A 272 ASN cc_start: 0.6116 (t0) cc_final: 0.5889 (m-40) outliers start: 18 outliers final: 11 residues processed: 90 average time/residue: 0.1860 time to fit residues: 22.8310 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.184389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137651 restraints weight = 7170.901| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.86 r_work: 0.3623 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6803 Z= 0.228 Angle : 0.660 13.193 9289 Z= 0.322 Chirality : 0.045 0.147 1019 Planarity : 0.005 0.055 1217 Dihedral : 5.493 57.306 968 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.68 % Allowed : 18.53 % Favored : 77.79 % 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: -0.46 (0.30), residues: 835 helix: 0.47 (0.58), residues: 75 sheet: -1.03 (0.38), residues: 187 loop : -0.07 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 468 HIS 0.009 0.001 HIS A 345 PHE 0.015 0.002 PHE A 31 TYR 0.011 0.002 TYR A 595 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 2) link_NAG-ASN : angle 2.72154 ( 6) link_BETA1-4 : bond 0.00151 ( 1) link_BETA1-4 : angle 2.39548 ( 3) hydrogen bonds : bond 0.03607 ( 166) hydrogen bonds : angle 5.68474 ( 453) metal coordination : bond 0.00355 ( 3) SS BOND : bond 0.00388 ( 11) SS BOND : angle 0.85440 ( 22) covalent geometry : bond 0.00558 ( 6786) covalent geometry : angle 0.65430 ( 9258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7179 (Cg_endo) cc_final: 0.6769 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7583 (mp) REVERT: A 140 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.8063 (mtm-85) REVERT: A 144 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7543 (tp) outliers start: 27 outliers final: 17 residues processed: 93 average time/residue: 0.1870 time to fit residues: 23.5877 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 730 ASP 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 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 47 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.187211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140761 restraints weight = 7049.409| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.82 r_work: 0.3668 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6803 Z= 0.135 Angle : 0.575 13.052 9289 Z= 0.281 Chirality : 0.043 0.140 1019 Planarity : 0.005 0.052 1217 Dihedral : 5.101 51.563 968 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -0.33 (0.30), residues: 835 helix: 0.55 (0.58), residues: 75 sheet: -0.98 (0.37), residues: 195 loop : 0.06 (0.28), 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 0.013 0.001 PHE A 511 TYR 0.010 0.001 TYR A 880 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 2) link_NAG-ASN : angle 2.20270 ( 6) link_BETA1-4 : bond 0.00010 ( 1) link_BETA1-4 : angle 2.14496 ( 3) hydrogen bonds : bond 0.03007 ( 166) hydrogen bonds : angle 5.38684 ( 453) metal coordination : bond 0.00201 ( 3) SS BOND : bond 0.00176 ( 11) SS BOND : angle 0.63789 ( 22) covalent geometry : bond 0.00332 ( 6786) covalent geometry : angle 0.57113 ( 9258) *********************** 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 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7185 (Cg_endo) cc_final: 0.6835 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7559 (mp) REVERT: A 140 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.8028 (mtm-85) REVERT: A 144 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7459 (tp) REVERT: A 275 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6605 (tp) outliers start: 26 outliers final: 16 residues processed: 88 average time/residue: 0.1711 time to fit residues: 21.0597 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 272 ASN 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 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: 8.9990 chunk 34 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 57 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.186989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141035 restraints weight = 6953.628| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.78 r_work: 0.3675 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6803 Z= 0.133 Angle : 0.567 12.825 9289 Z= 0.276 Chirality : 0.043 0.139 1019 Planarity : 0.005 0.052 1217 Dihedral : 5.041 50.552 968 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -0.27 (0.30), residues: 835 helix: 0.57 (0.58), residues: 75 sheet: -0.93 (0.37), residues: 195 loop : 0.10 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 468 HIS 0.010 0.001 HIS A 345 PHE 0.013 0.001 PHE A 511 TYR 0.008 0.001 TYR A 279 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 2) link_NAG-ASN : angle 2.22657 ( 6) link_BETA1-4 : bond 0.00174 ( 1) link_BETA1-4 : angle 2.16005 ( 3) hydrogen bonds : bond 0.02932 ( 166) hydrogen bonds : angle 5.33221 ( 453) metal coordination : bond 0.00168 ( 3) SS BOND : bond 0.00176 ( 11) SS BOND : angle 0.57787 ( 22) covalent geometry : bond 0.00328 ( 6786) covalent geometry : angle 0.56292 ( 9258) *********************** 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: 24 poor density : 69 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7129 (Cg_endo) cc_final: 0.6794 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7567 (mp) REVERT: A 140 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.8002 (mtm-85) REVERT: A 144 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7469 (tp) REVERT: A 275 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6488 (tp) outliers start: 24 outliers final: 18 residues processed: 89 average time/residue: 0.1683 time to fit residues: 20.6850 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 272 ASN 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 585 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.185357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139345 restraints weight = 7002.280| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.77 r_work: 0.3642 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6803 Z= 0.175 Angle : 0.602 13.158 9289 Z= 0.294 Chirality : 0.044 0.147 1019 Planarity : 0.005 0.053 1217 Dihedral : 5.163 50.869 968 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.81 % Allowed : 19.48 % 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: -0.37 (0.30), residues: 835 helix: 0.45 (0.58), residues: 75 sheet: -0.99 (0.37), residues: 195 loop : 0.04 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 468 HIS 0.006 0.001 HIS A 499 PHE 0.014 0.002 PHE A 31 TYR 0.010 0.001 TYR A 279 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 2) link_NAG-ASN : angle 2.36622 ( 6) link_BETA1-4 : bond 0.00142 ( 1) link_BETA1-4 : angle 2.19949 ( 3) hydrogen bonds : bond 0.03190 ( 166) hydrogen bonds : angle 5.43563 ( 453) metal coordination : bond 0.00273 ( 3) SS BOND : bond 0.00280 ( 11) SS BOND : angle 0.60706 ( 22) covalent geometry : bond 0.00431 ( 6786) covalent geometry : angle 0.59821 ( 9258) *********************** 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 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7178 (Cg_endo) cc_final: 0.6828 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7596 (mp) REVERT: A 140 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.8017 (mtm-85) REVERT: A 144 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7478 (tp) REVERT: A 275 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6512 (tp) REVERT: A 318 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6674 (mt-10) outliers start: 28 outliers final: 18 residues processed: 93 average time/residue: 0.1781 time to fit residues: 22.9437 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 730 ASP 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: 0.3980 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.0030 chunk 20 optimal weight: 0.0030 chunk 77 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.190956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145016 restraints weight = 6948.071| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.80 r_work: 0.3704 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6803 Z= 0.094 Angle : 0.555 12.287 9289 Z= 0.271 Chirality : 0.042 0.141 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.777 42.720 968 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.32 % Allowed : 21.66 % 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: -0.02 (0.30), residues: 835 helix: 1.04 (0.63), residues: 69 sheet: -0.72 (0.38), residues: 185 loop : 0.20 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 283 HIS 0.012 0.001 HIS A 345 PHE 0.012 0.001 PHE A 511 TYR 0.009 0.001 TYR A 145 ARG 0.003 0.000 ARG A 344 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 2) link_NAG-ASN : angle 1.94176 ( 6) link_BETA1-4 : bond 0.00211 ( 1) link_BETA1-4 : angle 2.04313 ( 3) hydrogen bonds : bond 0.02625 ( 166) hydrogen bonds : angle 5.09779 ( 453) metal coordination : bond 0.00064 ( 3) SS BOND : bond 0.00195 ( 11) SS BOND : angle 0.93627 ( 22) covalent geometry : bond 0.00229 ( 6786) covalent geometry : angle 0.55105 ( 9258) *********************** 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 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7111 (Cg_endo) cc_final: 0.6832 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7495 (mp) REVERT: A 272 ASN cc_start: 0.6004 (t0) cc_final: 0.5802 (m-40) REVERT: A 318 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6648 (mt-10) REVERT: A 664 SER cc_start: 0.8210 (t) cc_final: 0.7628 (m) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1683 time to fit residues: 19.3865 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 442 LEU 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 924 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.0040 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.190300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144205 restraints weight = 6958.095| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.78 r_work: 0.3691 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6803 Z= 0.115 Angle : 0.562 11.952 9289 Z= 0.275 Chirality : 0.042 0.142 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.549 22.024 967 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.59 % Allowed : 21.25 % 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: 0.01 (0.30), residues: 835 helix: 1.10 (0.63), residues: 69 sheet: -0.67 (0.38), residues: 185 loop : 0.20 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 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 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 2) link_NAG-ASN : angle 2.13906 ( 6) link_BETA1-4 : bond 0.00150 ( 1) link_BETA1-4 : angle 2.03770 ( 3) hydrogen bonds : bond 0.02699 ( 166) hydrogen bonds : angle 5.03908 ( 453) metal coordination : bond 0.00122 ( 3) SS BOND : bond 0.00223 ( 11) SS BOND : angle 1.04670 ( 22) covalent geometry : bond 0.00286 ( 6786) covalent geometry : angle 0.55724 ( 9258) *********************** 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 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7101 (Cg_endo) cc_final: 0.6844 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7534 (mp) REVERT: A 275 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6377 (tp) REVERT: A 318 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6680 (mt-10) REVERT: A 456 SER cc_start: 0.8329 (m) cc_final: 0.8051 (p) REVERT: A 664 SER cc_start: 0.8181 (t) cc_final: 0.7587 (m) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.1678 time to fit residues: 19.3285 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.186852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139583 restraints weight = 7134.366| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.86 r_work: 0.3670 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6803 Z= 0.168 Angle : 0.608 12.435 9289 Z= 0.298 Chirality : 0.044 0.144 1019 Planarity : 0.005 0.052 1217 Dihedral : 4.825 23.829 967 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.59 % Allowed : 21.12 % 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: -0.13 (0.30), residues: 835 helix: 0.76 (0.62), residues: 69 sheet: -0.73 (0.38), residues: 184 loop : 0.13 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 468 HIS 0.016 0.001 HIS A 345 PHE 0.014 0.002 PHE A 31 TYR 0.011 0.001 TYR A 595 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 2) link_NAG-ASN : angle 2.39077 ( 6) link_BETA1-4 : bond 0.00135 ( 1) link_BETA1-4 : angle 2.19603 ( 3) hydrogen bonds : bond 0.03092 ( 166) hydrogen bonds : angle 5.25618 ( 453) metal coordination : bond 0.00301 ( 3) SS BOND : bond 0.00303 ( 11) SS BOND : angle 1.02619 ( 22) covalent geometry : bond 0.00410 ( 6786) covalent geometry : angle 0.60310 ( 9258) ********************** 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 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7188 (Cg_endo) cc_final: 0.6879 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7534 (mp) REVERT: A 275 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6458 (tp) REVERT: A 318 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6734 (mt-10) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.1686 time to fit residues: 19.4665 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 790 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 924 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 36 optimal weight: 0.0270 chunk 32 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.191204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144461 restraints weight = 7032.618| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.87 r_work: 0.3692 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6803 Z= 0.104 Angle : 0.550 12.093 9289 Z= 0.270 Chirality : 0.042 0.138 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.475 20.162 967 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.04 % Allowed : 21.53 % Favored : 76.43 % 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: 0.11 (0.31), residues: 835 helix: 0.99 (0.63), residues: 70 sheet: -0.64 (0.38), residues: 185 loop : 0.32 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 283 HIS 0.007 0.001 HIS A 499 PHE 0.011 0.001 PHE A 511 TYR 0.007 0.001 TYR A 145 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 1.94027 ( 6) link_BETA1-4 : bond 0.00204 ( 1) link_BETA1-4 : angle 1.99230 ( 3) hydrogen bonds : bond 0.02639 ( 166) hydrogen bonds : angle 4.95832 ( 453) metal coordination : bond 0.00121 ( 3) SS BOND : bond 0.00133 ( 11) SS BOND : angle 1.00299 ( 22) covalent geometry : bond 0.00257 ( 6786) covalent geometry : angle 0.54491 ( 9258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.46 seconds wall clock time: 61 minutes 58.70 seconds (3718.70 seconds total)