Starting phenix.real_space_refine on Wed Feb 4 06:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ue3_64076/02_2026/9ue3_64076.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ue3_64076/02_2026/9ue3_64076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ue3_64076/02_2026/9ue3_64076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ue3_64076/02_2026/9ue3_64076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ue3_64076/02_2026/9ue3_64076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ue3_64076/02_2026/9ue3_64076.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5623 2.51 5 N 1416 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8896 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8435 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 35, 'TRANS': 1058} Chain breaks: 7 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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: "F" 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: "G" 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: "H" 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: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 2.26, per 1000 atoms: 0.25 Number of scatterers: 8896 At special positions: 0 Unit cell: (119.07, 90.72, 157.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1814 8.00 N 1416 7.00 C 5623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 403 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 740 " distance=2.04 Simple disulfide: pdb=" SG CYS A 801 " - pdb=" SG CYS A 813 " distance=2.03 Simple disulfide: pdb=" SG CYS A 864 " - pdb=" SG CYS A 886 " distance=2.04 Simple disulfide: pdb=" SG CYS A 869 " - pdb=" SG CYS A 875 " distance=2.02 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A 998 " distance=2.03 Simple disulfide: pdb=" SG CYS A1190 " - pdb=" SG CYS A1201 " distance=2.04 Simple disulfide: pdb=" SG CYS A1240 " - pdb=" SG CYS A1291 " distance=2.03 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1501 " - " ASN A 234 " " NAG A1502 " - " ASN A 241 " " NAG A1503 " - " ASN A 337 " " NAG A1504 " - " ASN A 707 " " NAG A1505 " - " ASN A 783 " " NAG A1506 " - " ASN A1297 " " NAG A1507 " - " ASN A 483 " " NAG A1508 " - " ASN A 519 " " NAG A1509 " - " ASN A 557 " " NAG A1510 " - " ASN A 837 " " NAG A1511 " - " ASN A 843 " " NAG A1512 " - " ASN A 565 " " NAG A1513 " - " ASN A 408 " " NAG A1514 " - " ASN A 535 " " NAG A1515 " - " ASN A 348 " " NAG B 1 " - " ASN A1077 " " NAG C 1 " - " ASN A 288 " " NAG E 1 " - " ASN A 365 " " NAG F 1 " - " ASN A 452 " " NAG G 1 " - " ASN A 728 " " NAG H 1 " - " ASN A 924 " " NAG I 1 " - " ASN A1203 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 276.3 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 23.9% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.602A pdb=" N SER A 46 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 47' Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.590A pdb=" N CYS A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 459 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 882 through 908 removed outlier: 3.784A pdb=" N CYS A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 930 through 934 Processing helix chain 'A' and resid 943 through 951 removed outlier: 4.855A pdb=" N ASP A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 971 Processing helix chain 'A' and resid 995 through 1002 Processing helix chain 'A' and resid 1010 through 1028 removed outlier: 3.541A pdb=" N ALA A1014 " --> pdb=" O GLY A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1054 removed outlier: 3.717A pdb=" N ALA A1045 " --> pdb=" O PRO A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1082 removed outlier: 3.615A pdb=" N LEU A1067 " --> pdb=" O ASN A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1113 Processing helix chain 'A' and resid 1114 through 1123 Processing helix chain 'A' and resid 1124 through 1126 No H-bonds generated for 'chain 'A' and resid 1124 through 1126' Processing helix chain 'A' and resid 1134 through 1142 Processing helix chain 'A' and resid 1143 through 1190 removed outlier: 3.525A pdb=" N ALA A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 299 removed outlier: 3.548A pdb=" N ASN A 483 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU A 477 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 304 through 311 removed outlier: 5.476A pdb=" N ILE A 305 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER A 468 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 307 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP A 462 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 463 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 441 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE A 435 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 316 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 322 removed outlier: 4.520A pdb=" N ASN A 452 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 361 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THR A 360 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS A 376 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 362 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 405 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR A 414 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 511 removed outlier: 3.824A pdb=" N GLY A 755 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 749 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 769 " --> pdb=" O SER A 780 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 520 through 523 removed outlier: 4.351A pdb=" N ILE A 734 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU A 724 " --> pdb=" O VAL A 737 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 725 " --> pdb=" O TYR A 716 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 552 removed outlier: 6.636A pdb=" N TYR A 659 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 631 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 661 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 629 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU A 663 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 665 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 625 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 559 removed outlier: 5.689A pdb=" N VAL A 654 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA A 646 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 656 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 605 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 803 through 807 removed outlier: 3.642A pdb=" N ILE A 805 " --> pdb=" O VAL A 812 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 837 through 841 removed outlier: 5.624A pdb=" N THR A1234 " --> pdb=" O ARG A1261 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A1261 " --> pdb=" O THR A1234 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A1259 " --> pdb=" O TRP A1236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 844 through 854 removed outlier: 5.983A pdb=" N LEU A1225 " --> pdb=" O HIS A1206 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N HIS A1206 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 860 through 862 Processing sheet with id=AB4, first strand: chain 'A' and resid 1285 through 1288 removed outlier: 5.787A pdb=" N CYS A1240 " --> pdb=" O ALA A1298 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 972 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: 1.79 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2448 1.33 - 1.46: 2043 1.46 - 1.58: 4526 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 9073 Sorted by residual: bond pdb=" CA GLU A 253 " pdb=" C GLU A 253 " ideal model delta sigma weight residual 1.524 1.490 0.035 1.22e-02 6.72e+03 8.05e+00 bond pdb=" N THR A 62 " pdb=" CA THR A 62 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.02e+00 bond pdb=" N GLN A 230 " pdb=" CA GLN A 230 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.01e+00 bond pdb=" CA ASN A 843 " pdb=" C ASN A 843 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.28e-02 6.10e+03 7.56e+00 bond pdb=" CA VAL A 671 " pdb=" C VAL A 671 " ideal model delta sigma weight residual 1.524 1.498 0.027 1.05e-02 9.07e+03 6.61e+00 ... (remaining 9068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 11969 2.48 - 4.96: 329 4.96 - 7.44: 55 7.44 - 9.92: 11 9.92 - 12.40: 4 Bond angle restraints: 12368 Sorted by residual: angle pdb=" N THR A 248 " pdb=" CA THR A 248 " pdb=" C THR A 248 " ideal model delta sigma weight residual 109.85 117.71 -7.86 1.58e+00 4.01e-01 2.47e+01 angle pdb=" N LEU A 211 " pdb=" CA LEU A 211 " pdb=" C LEU A 211 " ideal model delta sigma weight residual 110.80 100.27 10.53 2.13e+00 2.20e-01 2.45e+01 angle pdb=" N VAL A 683 " pdb=" CA VAL A 683 " pdb=" C VAL A 683 " ideal model delta sigma weight residual 108.17 114.87 -6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" N GLU A 320 " pdb=" CA GLU A 320 " pdb=" C GLU A 320 " ideal model delta sigma weight residual 108.73 100.94 7.79 1.63e+00 3.76e-01 2.29e+01 angle pdb=" N PRO A 672 " pdb=" CA PRO A 672 " pdb=" C PRO A 672 " ideal model delta sigma weight residual 112.47 122.27 -9.80 2.06e+00 2.36e-01 2.26e+01 ... (remaining 12363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 5371 21.91 - 43.82: 311 43.82 - 65.73: 42 65.73 - 87.65: 25 87.65 - 109.56: 12 Dihedral angle restraints: 5761 sinusoidal: 2589 harmonic: 3172 Sorted by residual: dihedral pdb=" C VAL A 232 " pdb=" N VAL A 232 " pdb=" CA VAL A 232 " pdb=" CB VAL A 232 " ideal model delta harmonic sigma weight residual -122.00 -140.43 18.43 0 2.50e+00 1.60e-01 5.43e+01 dihedral pdb=" N VAL A 232 " pdb=" C VAL A 232 " pdb=" CA VAL A 232 " pdb=" CB VAL A 232 " ideal model delta harmonic sigma weight residual 123.40 139.40 -16.00 0 2.50e+00 1.60e-01 4.10e+01 dihedral pdb=" N THR A 210 " pdb=" C THR A 210 " pdb=" CA THR A 210 " pdb=" CB THR A 210 " ideal model delta harmonic sigma weight residual 123.40 138.81 -15.41 0 2.50e+00 1.60e-01 3.80e+01 ... (remaining 5758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1426 0.122 - 0.245: 80 0.245 - 0.367: 20 0.367 - 0.489: 5 0.489 - 0.612: 2 Chirality restraints: 1533 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.71e+02 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 1530 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1506 " -0.336 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG A1506 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1506 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG A1506 " 0.513 2.00e-02 2.50e+03 pdb=" O7 NAG A1506 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1501 " 0.316 2.00e-02 2.50e+03 2.72e-01 9.28e+02 pdb=" C7 NAG A1501 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A1501 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG A1501 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG A1501 " 0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1514 " 0.278 2.00e-02 2.50e+03 2.32e-01 6.71e+02 pdb=" C7 NAG A1514 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1514 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A1514 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG A1514 " 0.002 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1866 2.78 - 3.31: 7732 3.31 - 3.84: 14169 3.84 - 4.37: 16328 4.37 - 4.90: 28379 Nonbonded interactions: 68474 Sorted by model distance: nonbonded pdb=" OD1 ASP A 981 " pdb=" N GLY A1010 " model vdw 2.244 3.120 nonbonded pdb=" O SER A 421 " pdb=" OG SER A 421 " model vdw 2.250 3.040 nonbonded pdb=" O ILE A 201 " pdb=" NE2 GLN A 330 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR A 773 " pdb=" O PHE A 776 " model vdw 2.266 3.040 nonbonded pdb=" O CYS A 987 " pdb=" OH TYR A1002 " model vdw 2.275 3.040 ... (remaining 68469 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 9.800 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.070 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.006 0.058 9119 Z= 0.349 Angle : 1.014 12.404 12494 Z= 0.564 Chirality : 0.075 0.612 1533 Planarity : 0.020 0.289 1539 Dihedral : 15.318 109.556 3695 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.66 % Favored : 94.06 % Rotamer: Outliers : 1.70 % Allowed : 5.54 % Favored : 92.76 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.22), residues: 1078 helix: -0.04 (0.31), residues: 242 sheet: -0.35 (0.30), residues: 258 loop : -2.19 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.018 0.002 TYR A 238 PHE 0.020 0.002 PHE A 266 TRP 0.011 0.001 TRP A 462 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 9073) covalent geometry : angle 0.98580 (12368) SS BOND : bond 0.00432 ( 12) SS BOND : angle 1.77394 ( 24) hydrogen bonds : bond 0.11026 ( 326) hydrogen bonds : angle 5.37775 ( 972) link_ALPHA1-3 : bond 0.00250 ( 2) link_ALPHA1-3 : angle 1.51775 ( 6) link_BETA1-4 : bond 0.00261 ( 10) link_BETA1-4 : angle 1.53956 ( 30) link_NAG-ASN : bond 0.00769 ( 22) link_NAG-ASN : angle 3.17060 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.346 Fit side-chains REVERT: A 238 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5820 (t80) outliers start: 16 outliers final: 1 residues processed: 162 average time/residue: 0.5774 time to fit residues: 99.8772 Evaluate side-chains 72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 1152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 282 ASN A 301 GLN A1064 GLN A1094 GLN A1111 ASN A1173 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070485 restraints weight = 20378.259| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.20 r_work: 0.2901 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9119 Z= 0.178 Angle : 0.675 11.709 12494 Z= 0.336 Chirality : 0.046 0.203 1533 Planarity : 0.004 0.040 1539 Dihedral : 9.749 77.818 1879 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.66 % Allowed : 12.57 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.24), residues: 1078 helix: 1.39 (0.34), residues: 239 sheet: -0.13 (0.32), residues: 260 loop : -1.73 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 647 TYR 0.014 0.001 TYR A1020 PHE 0.011 0.001 PHE A 206 TRP 0.010 0.001 TRP A 430 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9073) covalent geometry : angle 0.65260 (12368) SS BOND : bond 0.00238 ( 12) SS BOND : angle 1.32551 ( 24) hydrogen bonds : bond 0.04734 ( 326) hydrogen bonds : angle 4.40639 ( 972) link_ALPHA1-3 : bond 0.00974 ( 2) link_ALPHA1-3 : angle 2.96398 ( 6) link_BETA1-4 : bond 0.00418 ( 10) link_BETA1-4 : angle 1.61331 ( 30) link_NAG-ASN : bond 0.00324 ( 22) link_NAG-ASN : angle 1.95643 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.374 Fit side-chains REVERT: A 238 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 479 THR cc_start: 0.9447 (m) cc_final: 0.9175 (p) REVERT: A 1185 ASP cc_start: 0.8812 (m-30) cc_final: 0.8594 (m-30) outliers start: 25 outliers final: 6 residues processed: 85 average time/residue: 0.5279 time to fit residues: 48.4296 Evaluate side-chains 70 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 1152 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A1064 GLN A1094 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.070556 restraints weight = 20262.472| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.21 r_work: 0.2905 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9119 Z= 0.135 Angle : 0.585 9.016 12494 Z= 0.298 Chirality : 0.043 0.161 1533 Planarity : 0.004 0.041 1539 Dihedral : 6.883 58.009 1879 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.34 % Allowed : 13.53 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 1078 helix: 2.07 (0.35), residues: 238 sheet: -0.05 (0.31), residues: 282 loop : -1.51 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 647 TYR 0.014 0.001 TYR A1020 PHE 0.010 0.001 PHE A 206 TRP 0.006 0.001 TRP A 430 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9073) covalent geometry : angle 0.56722 (12368) SS BOND : bond 0.00278 ( 12) SS BOND : angle 1.08287 ( 24) hydrogen bonds : bond 0.04273 ( 326) hydrogen bonds : angle 4.20557 ( 972) link_ALPHA1-3 : bond 0.00956 ( 2) link_ALPHA1-3 : angle 1.51231 ( 6) link_BETA1-4 : bond 0.00573 ( 10) link_BETA1-4 : angle 1.56700 ( 30) link_NAG-ASN : bond 0.00158 ( 22) link_NAG-ASN : angle 1.67526 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.367 Fit side-chains REVERT: A 215 ARG cc_start: 0.7922 (tpm-80) cc_final: 0.7640 (tpm-80) REVERT: A 238 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: A 292 PHE cc_start: 0.8658 (m-80) cc_final: 0.8351 (m-80) REVERT: A 479 THR cc_start: 0.9432 (m) cc_final: 0.9169 (p) REVERT: A 542 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8077 (mmm) REVERT: A 853 MET cc_start: 0.9089 (mmm) cc_final: 0.8853 (mmt) REVERT: A 957 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8673 (tptp) outliers start: 22 outliers final: 9 residues processed: 79 average time/residue: 0.5190 time to fit residues: 44.2469 Evaluate side-chains 67 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 685 HIS A1064 GLN A1094 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070525 restraints weight = 20675.139| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.24 r_work: 0.2903 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9119 Z= 0.126 Angle : 0.543 8.783 12494 Z= 0.279 Chirality : 0.042 0.167 1533 Planarity : 0.004 0.044 1539 Dihedral : 6.013 59.161 1879 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.88 % Allowed : 13.95 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1078 helix: 2.33 (0.36), residues: 238 sheet: -0.14 (0.32), residues: 272 loop : -1.33 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 647 TYR 0.017 0.001 TYR A 692 PHE 0.010 0.001 PHE A 48 TRP 0.006 0.001 TRP A 430 HIS 0.002 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9073) covalent geometry : angle 0.52485 (12368) SS BOND : bond 0.00147 ( 12) SS BOND : angle 1.00453 ( 24) hydrogen bonds : bond 0.04166 ( 326) hydrogen bonds : angle 4.11538 ( 972) link_ALPHA1-3 : bond 0.01066 ( 2) link_ALPHA1-3 : angle 1.90836 ( 6) link_BETA1-4 : bond 0.00388 ( 10) link_BETA1-4 : angle 1.53254 ( 30) link_NAG-ASN : bond 0.00160 ( 22) link_NAG-ASN : angle 1.52990 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.353 Fit side-chains REVERT: A 53 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7853 (t) REVERT: A 215 ARG cc_start: 0.8006 (tpm-80) cc_final: 0.7666 (tpm-80) REVERT: A 238 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: A 292 PHE cc_start: 0.8659 (m-80) cc_final: 0.8353 (m-80) REVERT: A 479 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9175 (p) REVERT: A 955 ASN cc_start: 0.8909 (p0) cc_final: 0.8682 (p0) REVERT: A 957 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8683 (tptp) REVERT: A 1232 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9307 (m) outliers start: 27 outliers final: 10 residues processed: 85 average time/residue: 0.5638 time to fit residues: 51.5428 Evaluate side-chains 72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 0.0970 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 GLN A1094 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071237 restraints weight = 20447.632| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.22 r_work: 0.2916 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9119 Z= 0.108 Angle : 0.518 8.664 12494 Z= 0.265 Chirality : 0.042 0.166 1533 Planarity : 0.004 0.045 1539 Dihedral : 5.227 57.762 1879 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.56 % Allowed : 14.16 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1078 helix: 2.55 (0.36), residues: 238 sheet: -0.13 (0.32), residues: 270 loop : -1.25 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1177 TYR 0.013 0.001 TYR A1020 PHE 0.008 0.001 PHE A1260 TRP 0.006 0.001 TRP A 462 HIS 0.001 0.000 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9073) covalent geometry : angle 0.50375 (12368) SS BOND : bond 0.00138 ( 12) SS BOND : angle 0.87506 ( 24) hydrogen bonds : bond 0.03858 ( 326) hydrogen bonds : angle 3.96365 ( 972) link_ALPHA1-3 : bond 0.01101 ( 2) link_ALPHA1-3 : angle 1.51265 ( 6) link_BETA1-4 : bond 0.00407 ( 10) link_BETA1-4 : angle 1.34627 ( 30) link_NAG-ASN : bond 0.00148 ( 22) link_NAG-ASN : angle 1.39953 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.426 Fit side-chains REVERT: A 53 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.8013 (t) REVERT: A 238 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 292 PHE cc_start: 0.8624 (m-80) cc_final: 0.8343 (m-80) REVERT: A 383 GLU cc_start: 0.2426 (OUTLIER) cc_final: 0.2220 (tp30) REVERT: A 479 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9138 (p) REVERT: A 955 ASN cc_start: 0.8881 (p0) cc_final: 0.8650 (p0) REVERT: A 957 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8726 (tptp) REVERT: A 1232 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9324 (m) outliers start: 24 outliers final: 6 residues processed: 87 average time/residue: 0.5216 time to fit residues: 49.0535 Evaluate side-chains 72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 282 ASN A1064 GLN A1094 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.067340 restraints weight = 20816.699| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.21 r_work: 0.2839 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9119 Z= 0.257 Angle : 0.627 8.407 12494 Z= 0.320 Chirality : 0.045 0.172 1533 Planarity : 0.004 0.048 1539 Dihedral : 5.598 59.148 1877 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.77 % Allowed : 15.55 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1078 helix: 2.31 (0.36), residues: 237 sheet: -0.14 (0.33), residues: 250 loop : -1.33 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 215 TYR 0.016 0.002 TYR A 807 PHE 0.011 0.001 PHE A1208 TRP 0.009 0.001 TRP A 430 HIS 0.004 0.001 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 9073) covalent geometry : angle 0.60456 (12368) SS BOND : bond 0.00244 ( 12) SS BOND : angle 1.65028 ( 24) hydrogen bonds : bond 0.04892 ( 326) hydrogen bonds : angle 4.33556 ( 972) link_ALPHA1-3 : bond 0.00839 ( 2) link_ALPHA1-3 : angle 1.97079 ( 6) link_BETA1-4 : bond 0.00333 ( 10) link_BETA1-4 : angle 1.73390 ( 30) link_NAG-ASN : bond 0.00348 ( 22) link_NAG-ASN : angle 1.79255 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.331 Fit side-chains REVERT: A 53 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7985 (t) REVERT: A 383 GLU cc_start: 0.2745 (OUTLIER) cc_final: 0.1544 (mm-30) REVERT: A 853 MET cc_start: 0.9092 (mmm) cc_final: 0.8842 (mmt) REVERT: A 957 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8777 (tptp) REVERT: A 1232 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9309 (m) outliers start: 26 outliers final: 11 residues processed: 81 average time/residue: 0.5266 time to fit residues: 45.9783 Evaluate side-chains 72 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A1064 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.068769 restraints weight = 20753.849| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.23 r_work: 0.2868 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9119 Z= 0.143 Angle : 0.554 8.678 12494 Z= 0.286 Chirality : 0.042 0.162 1533 Planarity : 0.004 0.048 1539 Dihedral : 5.094 53.571 1875 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.70 % Allowed : 16.93 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1078 helix: 2.45 (0.36), residues: 237 sheet: -0.07 (0.33), residues: 250 loop : -1.32 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 215 TYR 0.013 0.001 TYR A1020 PHE 0.009 0.001 PHE A 292 TRP 0.006 0.001 TRP A 430 HIS 0.002 0.000 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9073) covalent geometry : angle 0.53638 (12368) SS BOND : bond 0.00193 ( 12) SS BOND : angle 1.18132 ( 24) hydrogen bonds : bond 0.04334 ( 326) hydrogen bonds : angle 4.15558 ( 972) link_ALPHA1-3 : bond 0.00885 ( 2) link_ALPHA1-3 : angle 1.40800 ( 6) link_BETA1-4 : bond 0.00355 ( 10) link_BETA1-4 : angle 1.49206 ( 30) link_NAG-ASN : bond 0.00166 ( 22) link_NAG-ASN : angle 1.55840 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.287 Fit side-chains REVERT: A 53 SER cc_start: 0.8201 (p) cc_final: 0.7951 (t) REVERT: A 292 PHE cc_start: 0.8660 (m-80) cc_final: 0.8363 (m-80) REVERT: A 383 GLU cc_start: 0.2802 (OUTLIER) cc_final: 0.1598 (mm-30) REVERT: A 853 MET cc_start: 0.9043 (mmm) cc_final: 0.8765 (mmt) REVERT: A 955 ASN cc_start: 0.9062 (p0) cc_final: 0.8848 (p0) REVERT: A 1232 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9349 (m) outliers start: 16 outliers final: 9 residues processed: 77 average time/residue: 0.4798 time to fit residues: 39.8550 Evaluate side-chains 70 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN A1064 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.069951 restraints weight = 20597.492| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.23 r_work: 0.2894 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9119 Z= 0.116 Angle : 0.550 11.838 12494 Z= 0.281 Chirality : 0.042 0.162 1533 Planarity : 0.004 0.047 1539 Dihedral : 4.745 53.203 1875 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.92 % Allowed : 17.25 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1078 helix: 2.60 (0.36), residues: 238 sheet: -0.09 (0.33), residues: 250 loop : -1.26 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 215 TYR 0.013 0.001 TYR A 213 PHE 0.008 0.001 PHE A1260 TRP 0.006 0.001 TRP A 430 HIS 0.001 0.000 HIS A 685 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9073) covalent geometry : angle 0.53568 (12368) SS BOND : bond 0.00186 ( 12) SS BOND : angle 0.90903 ( 24) hydrogen bonds : bond 0.03949 ( 326) hydrogen bonds : angle 3.99114 ( 972) link_ALPHA1-3 : bond 0.00849 ( 2) link_ALPHA1-3 : angle 1.32951 ( 6) link_BETA1-4 : bond 0.00358 ( 10) link_BETA1-4 : angle 1.43512 ( 30) link_NAG-ASN : bond 0.00148 ( 22) link_NAG-ASN : angle 1.45015 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.359 Fit side-chains REVERT: A 53 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7943 (t) REVERT: A 292 PHE cc_start: 0.8609 (m-80) cc_final: 0.8331 (m-80) REVERT: A 383 GLU cc_start: 0.2917 (OUTLIER) cc_final: 0.1748 (mm-30) REVERT: A 568 ASP cc_start: 0.8840 (m-30) cc_final: 0.8558 (m-30) REVERT: A 853 MET cc_start: 0.9046 (mmm) cc_final: 0.8775 (mmt) REVERT: A 955 ASN cc_start: 0.8999 (p0) cc_final: 0.8797 (p0) REVERT: A 1232 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9349 (m) outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.4067 time to fit residues: 33.1453 Evaluate side-chains 75 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067782 restraints weight = 20468.938| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.18 r_work: 0.2858 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9119 Z= 0.207 Angle : 0.598 8.449 12494 Z= 0.304 Chirality : 0.043 0.163 1533 Planarity : 0.004 0.049 1539 Dihedral : 4.982 53.574 1875 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.92 % Allowed : 17.36 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1078 helix: 2.44 (0.36), residues: 237 sheet: -0.03 (0.34), residues: 244 loop : -1.28 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 215 TYR 0.015 0.001 TYR A 213 PHE 0.010 0.001 PHE A 292 TRP 0.008 0.001 TRP A 430 HIS 0.003 0.001 HIS A1206 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9073) covalent geometry : angle 0.57906 (12368) SS BOND : bond 0.00214 ( 12) SS BOND : angle 1.24868 ( 24) hydrogen bonds : bond 0.04575 ( 326) hydrogen bonds : angle 4.23763 ( 972) link_ALPHA1-3 : bond 0.00804 ( 2) link_ALPHA1-3 : angle 1.57439 ( 6) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.64265 ( 30) link_NAG-ASN : bond 0.00261 ( 22) link_NAG-ASN : angle 1.68819 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.249 Fit side-chains REVERT: A 53 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7947 (t) REVERT: A 292 PHE cc_start: 0.8646 (m-80) cc_final: 0.8366 (m-80) REVERT: A 383 GLU cc_start: 0.3531 (OUTLIER) cc_final: 0.2139 (mm-30) REVERT: A 853 MET cc_start: 0.9076 (mmm) cc_final: 0.8816 (mmt) REVERT: A 1232 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9329 (m) outliers start: 18 outliers final: 14 residues processed: 75 average time/residue: 0.4771 time to fit residues: 38.7669 Evaluate side-chains 74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.0070 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.087432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069937 restraints weight = 20403.453| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.17 r_work: 0.2900 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9119 Z= 0.109 Angle : 0.558 10.563 12494 Z= 0.285 Chirality : 0.042 0.160 1533 Planarity : 0.004 0.047 1539 Dihedral : 4.743 53.290 1875 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.49 % Allowed : 18.00 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1078 helix: 2.59 (0.36), residues: 238 sheet: -0.09 (0.33), residues: 246 loop : -1.23 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 215 TYR 0.021 0.001 TYR A 213 PHE 0.011 0.001 PHE A 48 TRP 0.005 0.001 TRP A 430 HIS 0.001 0.000 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9073) covalent geometry : angle 0.54414 (12368) SS BOND : bond 0.00171 ( 12) SS BOND : angle 0.91911 ( 24) hydrogen bonds : bond 0.04023 ( 326) hydrogen bonds : angle 4.04213 ( 972) link_ALPHA1-3 : bond 0.00854 ( 2) link_ALPHA1-3 : angle 1.25835 ( 6) link_BETA1-4 : bond 0.00376 ( 10) link_BETA1-4 : angle 1.40536 ( 30) link_NAG-ASN : bond 0.00169 ( 22) link_NAG-ASN : angle 1.45489 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.326 Fit side-chains REVERT: A 53 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7952 (t) REVERT: A 292 PHE cc_start: 0.8610 (m-80) cc_final: 0.8322 (m-80) REVERT: A 383 GLU cc_start: 0.3102 (OUTLIER) cc_final: 0.2105 (mm-30) REVERT: A 568 ASP cc_start: 0.8820 (m-30) cc_final: 0.8516 (m-30) REVERT: A 853 MET cc_start: 0.9039 (mmm) cc_final: 0.8763 (mmt) REVERT: A 1232 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9357 (m) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.4640 time to fit residues: 36.1579 Evaluate side-chains 69 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1152 ASP Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.068514 restraints weight = 20365.717| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.16 r_work: 0.2874 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9119 Z= 0.170 Angle : 0.570 8.381 12494 Z= 0.291 Chirality : 0.042 0.160 1533 Planarity : 0.004 0.047 1539 Dihedral : 4.837 53.384 1875 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.49 % Allowed : 18.00 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1078 helix: 2.49 (0.36), residues: 237 sheet: -0.05 (0.34), residues: 244 loop : -1.24 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 215 TYR 0.020 0.001 TYR A 213 PHE 0.011 0.001 PHE A 48 TRP 0.007 0.001 TRP A 430 HIS 0.002 0.001 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9073) covalent geometry : angle 0.55247 (12368) SS BOND : bond 0.00192 ( 12) SS BOND : angle 1.10514 ( 24) hydrogen bonds : bond 0.04347 ( 326) hydrogen bonds : angle 4.14760 ( 972) link_ALPHA1-3 : bond 0.00752 ( 2) link_ALPHA1-3 : angle 1.40722 ( 6) link_BETA1-4 : bond 0.00319 ( 10) link_BETA1-4 : angle 1.56807 ( 30) link_NAG-ASN : bond 0.00196 ( 22) link_NAG-ASN : angle 1.60049 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.42 seconds wall clock time: 43 minutes 38.02 seconds (2618.02 seconds total)