Starting phenix.real_space_refine on Thu Jul 24 22:50:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl1_40571/07_2025/8sl1_40571_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl1_40571/07_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_40571/07_2025/8sl1_40571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_2025/8sl1_40571.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_2025/8sl1_40571_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl1_40571/07_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-5711/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: 5.04, per 1000 atoms: 0.76 Number of scatterers: 6608 At special positions: 0 Unit cell: (78.942, 86.301, 107.709, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 45 16.00 O 1285 8.00 N 1118 7.00 C 4157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 580 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 769 " distance=2.04 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A 881 " - pdb=" SG CYS A 909 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 917 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1802 " - " ASN A 445 " " NAG B 1 " - " ASN A 328 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 930.2 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: 0.91 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: 1.93 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- 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 : 0.661 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: 0.2371 time to fit residues: 22.3418 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 : 0.663 ------------------------------------------------------------------------------- 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 = 0.189935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144609 restraints weight = 6929.757| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.79 r_work: 0.3715 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0901 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 11.108 9289 Z= 0.287 Chirality : 0.043 0.150 1019 Planarity : 0.005 0.059 1217 Dihedral : 5.379 59.729 972 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 0.00373 ( 2) link_NAG-ASN : angle 2.76469 ( 6) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 2.37749 ( 3) hydrogen bonds : bond 0.03220 ( 166) hydrogen bonds : angle 5.30314 ( 453) metal coordination : bond 0.00601 ( 3) SS BOND : bond 0.00227 ( 11) SS BOND : angle 0.83341 ( 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 : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7541 (mp) REVERT: A 166 MET cc_start: 0.5158 (ppp) cc_final: 0.4609 (ppp) outliers start: 20 outliers final: 11 residues processed: 92 average time/residue: 0.1818 time to fit residues: 22.9343 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 : 0.667 ------------------------------------------------------------------------------- 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: 0.4980 chunk 70 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.189367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143067 restraints weight = 7005.668| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.82 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: 0.7147 moved from start: 0.1211 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= 0.134 Angle : 0.566 11.496 9289 Z= 0.277 Chirality : 0.043 0.142 1019 Planarity : 0.005 0.049 1217 Dihedral : 5.090 57.442 969 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.59 % Allowed : 17.98 % 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: -0.13 (0.31), residues: 835 helix: 0.96 (0.60), residues: 75 sheet: -0.74 (0.38), residues: 185 loop : 0.09 (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 0.022 0.002 PHE A 740 TYR 0.022 0.001 TYR A 880 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 2.45499 ( 6) link_BETA1-4 : bond 0.00127 ( 1) link_BETA1-4 : angle 2.25965 ( 3) hydrogen bonds : bond 0.03014 ( 166) hydrogen bonds : angle 5.26581 ( 453) metal coordination : bond 0.00287 ( 3) SS BOND : bond 0.00192 ( 11) SS BOND : angle 0.72088 ( 22) covalent geometry : bond 0.00330 ( 6786) covalent geometry : angle 0.56103 ( 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.6939 (Cg_endo) cc_final: 0.6550 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7562 (mp) REVERT: A 140 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8024 (mtm-85) REVERT: A 272 ASN cc_start: 0.6116 (t0) cc_final: 0.5908 (m-40) outliers start: 19 outliers final: 12 residues processed: 92 average time/residue: 0.1788 time to fit residues: 22.3765 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 0 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.184727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138536 restraints weight = 7095.932| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.81 r_work: 0.3648 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6803 Z= 0.185 Angle : 0.614 12.741 9289 Z= 0.299 Chirality : 0.044 0.143 1019 Planarity : 0.005 0.054 1217 Dihedral : 5.261 55.937 968 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.95 % Allowed : 18.53 % 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: -0.31 (0.30), residues: 835 helix: 0.70 (0.58), residues: 75 sheet: -0.93 (0.38), residues: 187 loop : 0.01 (0.28), residues: 573 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 0.015 0.002 PHE A 31 TYR 0.013 0.001 TYR A 880 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 2.55401 ( 6) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 2.24928 ( 3) hydrogen bonds : bond 0.03328 ( 166) hydrogen bonds : angle 5.45706 ( 453) metal coordination : bond 0.00324 ( 3) SS BOND : bond 0.00305 ( 11) SS BOND : angle 0.77785 ( 22) covalent geometry : bond 0.00457 ( 6786) covalent geometry : angle 0.60915 ( 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: 29 poor density : 67 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7091 (Cg_endo) cc_final: 0.6713 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7559 (mp) REVERT: A 140 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8043 (mtm-85) REVERT: A 144 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7508 (tp) REVERT: A 276 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5635 (tp) outliers start: 29 outliers final: 16 residues processed: 93 average time/residue: 0.2062 time to fit residues: 26.5111 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 0.0770 chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 67 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.191495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145404 restraints weight = 6974.756| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.84 r_work: 0.3719 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6803 Z= 0.099 Angle : 0.534 11.809 9289 Z= 0.262 Chirality : 0.042 0.137 1019 Planarity : 0.005 0.048 1217 Dihedral : 4.752 49.794 968 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 19.62 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.31), residues: 835 helix: 0.85 (0.60), residues: 75 sheet: -0.62 (0.39), residues: 185 loop : 0.19 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.008 0.001 HIS A 499 PHE 0.025 0.001 PHE A 740 TYR 0.011 0.001 TYR A 880 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 1.95992 ( 6) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 2.02143 ( 3) hydrogen bonds : bond 0.02634 ( 166) hydrogen bonds : angle 5.12241 ( 453) metal coordination : bond 0.00111 ( 3) SS BOND : bond 0.00108 ( 11) SS BOND : angle 0.55179 ( 22) covalent geometry : bond 0.00241 ( 6786) covalent geometry : angle 0.53088 ( 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 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7059 (Cg_endo) cc_final: 0.6758 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7484 (mp) REVERT: A 276 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.5257 (tp) REVERT: A 664 SER cc_start: 0.8189 (t) cc_final: 0.7606 (m) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 0.1651 time to fit residues: 20.7221 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 433 MET Chi-restraints excluded: chain A residue 442 LEU 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: 7.9990 chunk 34 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.189693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.145844 restraints weight = 6978.988| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.83 r_work: 0.3702 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6803 Z= 0.123 Angle : 0.553 12.076 9289 Z= 0.268 Chirality : 0.042 0.143 1019 Planarity : 0.005 0.050 1217 Dihedral : 4.793 49.455 968 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.72 % Allowed : 20.57 % 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: 0.05 (0.31), residues: 835 helix: 1.17 (0.64), residues: 69 sheet: -0.62 (0.38), residues: 185 loop : 0.21 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 331 HIS 0.009 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 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 2.22849 ( 6) link_BETA1-4 : bond 0.00129 ( 1) link_BETA1-4 : angle 2.06955 ( 3) hydrogen bonds : bond 0.02816 ( 166) hydrogen bonds : angle 5.06445 ( 453) metal coordination : bond 0.00162 ( 3) SS BOND : bond 0.00162 ( 11) SS BOND : angle 0.52682 ( 22) covalent geometry : bond 0.00304 ( 6786) covalent geometry : angle 0.54932 ( 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 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7059 (Cg_endo) cc_final: 0.6788 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7536 (mp) REVERT: A 275 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6501 (tp) REVERT: A 318 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6704 (mt-10) REVERT: A 664 SER cc_start: 0.8164 (t) cc_final: 0.7587 (m) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.1819 time to fit residues: 22.5630 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 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 181 ASP 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 276 ILE Chi-restraints excluded: chain A residue 442 LEU 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: 4.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.187358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141257 restraints weight = 6970.021| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.80 r_work: 0.3664 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6803 Z= 0.145 Angle : 0.570 12.295 9289 Z= 0.277 Chirality : 0.043 0.154 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.873 49.465 968 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.27 % Allowed : 20.44 % 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: -0.00 (0.31), residues: 835 helix: 1.10 (0.64), residues: 69 sheet: -0.63 (0.39), residues: 185 loop : 0.18 (0.28), residues: 581 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 0.013 0.001 PHE A 511 TYR 0.009 0.001 TYR A 595 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 2) link_NAG-ASN : angle 2.26671 ( 6) link_BETA1-4 : bond 0.00091 ( 1) link_BETA1-4 : angle 2.12779 ( 3) hydrogen bonds : bond 0.02937 ( 166) hydrogen bonds : angle 5.15366 ( 453) metal coordination : bond 0.00243 ( 3) SS BOND : bond 0.00209 ( 11) SS BOND : angle 0.52548 ( 22) covalent geometry : bond 0.00360 ( 6786) covalent geometry : angle 0.56659 ( 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7095 (Cg_endo) cc_final: 0.6799 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7495 (mp) REVERT: A 275 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 276 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5703 (tp) REVERT: A 318 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6644 (mt-10) outliers start: 24 outliers final: 17 residues processed: 90 average time/residue: 0.1627 time to fit residues: 20.9184 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.187518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141053 restraints weight = 7059.160| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.81 r_work: 0.3655 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6803 Z= 0.153 Angle : 0.585 12.425 9289 Z= 0.285 Chirality : 0.043 0.154 1019 Planarity : 0.005 0.051 1217 Dihedral : 4.955 48.762 968 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.54 % Allowed : 20.30 % 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: -0.07 (0.30), residues: 835 helix: 1.02 (0.63), residues: 69 sheet: -0.71 (0.38), residues: 185 loop : 0.15 (0.28), residues: 581 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 0.013 0.001 PHE A 31 TYR 0.009 0.001 TYR A 595 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 2) link_NAG-ASN : angle 2.29868 ( 6) link_BETA1-4 : bond 0.00132 ( 1) link_BETA1-4 : angle 2.12978 ( 3) hydrogen bonds : bond 0.03022 ( 166) hydrogen bonds : angle 5.22369 ( 453) metal coordination : bond 0.00201 ( 3) SS BOND : bond 0.00222 ( 11) SS BOND : angle 0.52282 ( 22) covalent geometry : bond 0.00377 ( 6786) covalent geometry : angle 0.58126 ( 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7135 (Cg_endo) cc_final: 0.6832 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7507 (mp) REVERT: A 275 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6591 (tp) REVERT: A 276 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5753 (tp) REVERT: A 318 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6630 (mt-10) outliers start: 26 outliers final: 16 residues processed: 89 average time/residue: 0.1613 time to fit residues: 20.4492 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 : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 924 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.187253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140416 restraints weight = 7050.546| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.85 r_work: 0.3648 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6803 Z= 0.158 Angle : 0.592 13.146 9289 Z= 0.287 Chirality : 0.044 0.152 1019 Planarity : 0.005 0.052 1217 Dihedral : 4.998 48.396 968 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.86 % Allowed : 21.25 % Favored : 75.89 % 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 (0.30), residues: 835 helix: 0.98 (0.62), residues: 69 sheet: -0.73 (0.38), residues: 185 loop : 0.16 (0.28), residues: 581 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 0.031 0.002 PHE A 740 TYR 0.010 0.001 TYR A 595 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 2) link_NAG-ASN : angle 2.30189 ( 6) link_BETA1-4 : bond 0.00114 ( 1) link_BETA1-4 : angle 2.13365 ( 3) hydrogen bonds : bond 0.03068 ( 166) hydrogen bonds : angle 5.18113 ( 453) metal coordination : bond 0.00205 ( 3) SS BOND : bond 0.00207 ( 11) SS BOND : angle 0.52945 ( 22) covalent geometry : bond 0.00389 ( 6786) covalent geometry : angle 0.58843 ( 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 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.7125 (Cg_endo) cc_final: 0.6812 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 275 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6614 (tp) REVERT: A 318 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6635 (mt-10) REVERT: A 531 MET cc_start: 0.8460 (mtm) cc_final: 0.8215 (mtt) outliers start: 21 outliers final: 18 residues processed: 84 average time/residue: 0.1653 time to fit residues: 19.6162 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 199 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 501 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 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: 6.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.186011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138726 restraints weight = 7191.471| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.87 r_work: 0.3649 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6803 Z= 0.189 Angle : 0.644 14.056 9289 Z= 0.310 Chirality : 0.045 0.154 1019 Planarity : 0.005 0.053 1217 Dihedral : 5.188 49.295 968 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.72 % Allowed : 21.53 % Favored : 75.75 % 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: -0.25 (0.30), residues: 835 helix: 0.59 (0.58), residues: 75 sheet: -0.86 (0.37), residues: 194 loop : 0.09 (0.28), residues: 566 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 0.031 0.002 PHE A 740 TYR 0.012 0.001 TYR A 595 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 2) link_NAG-ASN : angle 2.44828 ( 6) link_BETA1-4 : bond 0.00091 ( 1) link_BETA1-4 : angle 2.20542 ( 3) hydrogen bonds : bond 0.03286 ( 166) hydrogen bonds : angle 5.33000 ( 453) metal coordination : bond 0.00265 ( 3) SS BOND : bond 0.00303 ( 11) SS BOND : angle 0.56634 ( 22) covalent geometry : bond 0.00464 ( 6786) covalent geometry : angle 0.64052 ( 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 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.710 Fit side-chains REVERT: A 68 PRO cc_start: 0.7218 (Cg_endo) cc_final: 0.6875 (Cg_exo) REVERT: A 70 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 275 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6699 (tp) REVERT: A 318 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6717 (mt-10) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1703 time to fit residues: 20.4552 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 501 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 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 16 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.186744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.142316 restraints weight = 7178.465| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.11 r_work: 0.3670 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6803 Z= 0.168 Angle : 0.614 13.294 9289 Z= 0.299 Chirality : 0.044 0.152 1019 Planarity : 0.005 0.052 1217 Dihedral : 5.122 43.930 968 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.59 % Allowed : 21.53 % Favored : 75.89 % 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: -0.28 (0.30), residues: 835 helix: 0.58 (0.58), residues: 75 sheet: -0.88 (0.37), residues: 194 loop : 0.07 (0.28), residues: 566 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 511 TYR 0.011 0.001 TYR A 595 ARG 0.007 0.001 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 2.33891 ( 6) link_BETA1-4 : bond 0.00119 ( 1) link_BETA1-4 : angle 2.18831 ( 3) hydrogen bonds : bond 0.03154 ( 166) hydrogen bonds : angle 5.30036 ( 453) metal coordination : bond 0.00211 ( 3) SS BOND : bond 0.00243 ( 11) SS BOND : angle 0.49849 ( 22) covalent geometry : bond 0.00414 ( 6786) covalent geometry : angle 0.61035 ( 9258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.76 seconds wall clock time: 58 minutes 27.92 seconds (3507.92 seconds total)