Starting phenix.real_space_refine on Thu Jul 2 08:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4x_24180/07_2026/7n4x_24180.map" } resolution = 3.33 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= 0.000 sd= 0.003 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 45 5.16 5 C 4992 2.51 5 N 1218 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7423 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} 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 chiralities: 2 Chain: "C" 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'CLR': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.71, per 1000 atoms: 0.22 Number of scatterers: 7647 At special positions: 0 Unit cell: (134.113, 93.296, 79.135, 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 45 16.00 O 1392 8.00 N 1218 7.00 C 4992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.02 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " 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 Atom "HETATM 7561 O5 NAG A1404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A 506 " " NAG A1404 " - " ASN A1075 " " NAG B 1 " - " ASN A 497 " " NAG C 1 " - " ASN A 909 " " NAG D 1 " - " ASN A1037 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 458.9 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 61.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.594A pdb=" N TRP A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.563A pdb=" N ILE A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.575A pdb=" N LEU A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.540A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 481 through 485 removed outlier: 4.004A pdb=" N CYS A 485 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.953A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.666A pdb=" N ALA A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 555' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 585 through 607 Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.618A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 649 removed outlier: 3.903A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 690 removed outlier: 3.787A pdb=" N LEU A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 724 removed outlier: 4.671A pdb=" N ASP A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 762 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 766 through 804 removed outlier: 3.563A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.670A pdb=" N PHE A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 864 removed outlier: 3.922A pdb=" N ARG A 846 " --> pdb=" O HIS A 842 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 881 through 893 removed outlier: 4.370A pdb=" N ASP A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.892A pdb=" N ALA A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1004 through 1017 Proline residue: A1013 - end of helix removed outlier: 3.548A pdb=" N ASN A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.549A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1107 Processing helix chain 'A' and resid 1108 through 1130 Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 4.442A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1225 removed outlier: 4.195A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1226 through 1230 Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1240 through 1254 Processing helix chain 'A' and resid 1256 through 1266 removed outlier: 3.927A pdb=" N VAL A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1276 removed outlier: 3.780A pdb=" N ALA A1274 " --> pdb=" O ASN A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.623A pdb=" N GLU A1282 " --> pdb=" O LYS A1278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.538A pdb=" N VAL A 410 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AA6, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id=AA7, first strand: chain 'A' and resid 979 through 980 removed outlier: 3.772A pdb=" N ARG A 968 " --> pdb=" O CYS A 980 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 7.179A pdb=" N ASN A1037 " --> pdb=" O LEU A1045 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1188 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: 1.02 Time building geometry restraints manager: 0.93 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: 1372 1.33 - 1.45: 1956 1.45 - 1.58: 4441 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 7838 Sorted by residual: bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.98e+01 bond pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta sigma weight residual 1.456 1.491 -0.036 8.70e-03 1.32e+04 1.67e+01 bond pdb=" N LEU A1109 " pdb=" CA LEU A1109 " ideal model delta sigma weight residual 1.463 1.491 -0.028 6.90e-03 2.10e+04 1.63e+01 bond pdb=" N LEU A1221 " pdb=" CA LEU A1221 " ideal model delta sigma weight residual 1.462 1.493 -0.032 8.50e-03 1.38e+04 1.38e+01 ... (remaining 7833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 6814 1.54 - 3.08: 2982 3.08 - 4.62: 779 4.62 - 6.16: 111 6.16 - 7.70: 6 Bond angle restraints: 10692 Sorted by residual: angle pdb=" N VAL A 813 " pdb=" CA VAL A 813 " pdb=" C VAL A 813 " ideal model delta sigma weight residual 113.10 108.53 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" C ARG A 846 " pdb=" N GLY A 847 " pdb=" CA GLY A 847 " ideal model delta sigma weight residual 119.94 124.95 -5.01 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C MET A 684 " pdb=" N GLY A 685 " pdb=" CA GLY A 685 " ideal model delta sigma weight residual 119.94 124.94 -5.00 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 124.91 -4.93 1.11e+00 8.12e-01 1.97e+01 angle pdb=" N ARG A1279 " pdb=" CA ARG A1279 " pdb=" C ARG A1279 " ideal model delta sigma weight residual 113.28 107.87 5.41 1.22e+00 6.72e-01 1.97e+01 ... (remaining 10687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 4069 17.36 - 34.72: 369 34.72 - 52.09: 93 52.09 - 69.45: 15 69.45 - 86.81: 6 Dihedral angle restraints: 4552 sinusoidal: 1776 harmonic: 2776 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CA PRO A 815 " pdb=" C PRO A 815 " pdb=" N GLN A 816 " pdb=" CA GLN A 816 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CB CYS A 980 " pdb=" SG CYS A 980 " pdb=" SG CYS A 989 " pdb=" CB CYS A 989 " ideal model delta sinusoidal sigma weight residual 93.00 53.79 39.21 1 1.00e+01 1.00e-02 2.16e+01 ... (remaining 4549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.938: 1269 0.938 - 1.875: 2 1.875 - 2.813: 1 2.813 - 3.750: 0 3.750 - 4.688: 2 Chirality restraints: 1274 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 2.29 -4.69 2.00e-02 2.50e+03 5.49e+04 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 1.70 -4.10 2.00e-01 2.50e+01 4.21e+02 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 -0.48 -1.92 2.00e-01 2.50e+01 9.20e+01 ... (remaining 1271 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.247 2.00e-02 2.50e+03 2.05e-01 5.28e+02 pdb=" C7 NAG B 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.341 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 431 " -0.115 2.00e-02 2.50e+03 1.88e-01 4.41e+02 pdb=" CG ASN A 431 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 431 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 431 " 0.336 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 909 " -0.149 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" CG ASN A 909 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 909 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 909 " 0.265 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.202 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 124 2.69 - 3.24: 7080 3.24 - 3.79: 11687 3.79 - 4.35: 15572 4.35 - 4.90: 27215 Nonbonded interactions: 61678 Sorted by model distance: nonbonded pdb=" OG SER A 912 " pdb=" O5 NAG C 1 " model vdw 2.134 3.040 nonbonded pdb=" OG SER A 912 " pdb=" O6 NAG C 1 " model vdw 2.148 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.315 3.040 nonbonded pdb=" O GLY A 710 " pdb=" NE2 GLN A 787 " model vdw 2.323 3.120 nonbonded pdb=" O THR A 629 " pdb=" NE2 GLN A 700 " model vdw 2.384 3.120 ... (remaining 61673 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.014 0.111 7854 Z= 1.068 Angle : 1.914 40.299 10734 Z= 1.343 Chirality : 0.211 4.688 1274 Planarity : 0.009 0.205 1321 Dihedral : 14.675 86.812 2744 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.23 % Allowed : 7.40 % Favored : 91.37 % 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: -3.15 (0.23), residues: 951 helix: -1.73 (0.18), residues: 516 sheet: -2.85 (0.54), residues: 62 loop : -2.28 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 606 TYR 0.025 0.002 TYR A 646 PHE 0.039 0.003 PHE A 791 TRP 0.016 0.002 TRP A 960 HIS 0.007 0.002 HIS A1053 Details of bonding type rmsd/Z covalent geometry : bond 0.01389 / 1.07 ( 7838) covalent geometry : angle 1.76280 / 1.32 (10692) SS BOND : bond 0.00404 / 0.18 ( 6) SS BOND : angle 1.21169 / 0.73 ( 12) hydrogen bonds : bond 0.15939 / 10.61 ( 412) hydrogen bonds : angle 6.71126 / 4.58 ( 1188) link_BETA1-4 : bond 0.00017 / 0.01 ( 3) link_BETA1-4 : angle 0.48376 / 0.23 ( 9) link_NAG-ASN : bond 0.05685 / 2.65 ( 7) link_NAG-ASN : angle 17.00929 / 14.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6880 (m100) cc_final: 0.6438 (m-10) REVERT: A 483 TYR cc_start: 0.7814 (m-80) cc_final: 0.7557 (m-80) REVERT: A 610 MET cc_start: 0.7717 (ttm) cc_final: 0.7166 (ttm) REVERT: A 657 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.5110 (t60) REVERT: A 943 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7224 (mt0) REVERT: A 1091 GLU cc_start: 0.7135 (tt0) cc_final: 0.6889 (tt0) REVERT: A 1218 MET cc_start: 0.7734 (mmt) cc_final: 0.7510 (mmm) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.0643 time to fit residues: 10.1721 Evaluate side-chains 77 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN A 397 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102073 restraints weight = 9108.837| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.47 r_work: 0.2948 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7854 Z= 0.144 Angle : 0.720 13.993 10734 Z= 0.325 Chirality : 0.044 0.382 1274 Planarity : 0.004 0.031 1321 Dihedral : 7.085 80.624 1064 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.97 % Allowed : 9.99 % Favored : 88.04 % 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: -0.95 (0.27), residues: 951 helix: 0.18 (0.22), residues: 550 sheet: -1.83 (0.57), residues: 63 loop : -1.62 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 693 TYR 0.016 0.001 TYR A 886 PHE 0.015 0.001 PHE A 791 TRP 0.014 0.001 TRP A 960 HIS 0.005 0.002 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7838) covalent geometry : angle 0.66248 / 0.31 (10692) SS BOND : bond 0.00284 / 0.15 ( 6) SS BOND : angle 0.99651 / 0.59 ( 12) hydrogen bonds : bond 0.04576 / 3.10 ( 412) hydrogen bonds : angle 4.53585 / 3.07 ( 1188) link_BETA1-4 : bond 0.00825 / 0.42 ( 3) link_BETA1-4 : angle 1.87715 / 1.05 ( 9) link_NAG-ASN : bond 0.00491 / 0.24 ( 7) link_NAG-ASN : angle 6.26904 / 5.44 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.186 Fit side-chains REVERT: A 351 TRP cc_start: 0.7586 (m100) cc_final: 0.7299 (m-10) REVERT: A 560 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8265 (mtpt) REVERT: A 657 TRP cc_start: 0.6693 (OUTLIER) cc_final: 0.5171 (t60) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 0.0586 time to fit residues: 8.6746 Evaluate side-chains 81 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103179 restraints weight = 9029.714| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.44 r_work: 0.2994 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.137 Angle : 0.604 9.366 10734 Z= 0.284 Chirality : 0.041 0.281 1274 Planarity : 0.004 0.032 1321 Dihedral : 6.561 75.810 1062 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.48 % Allowed : 12.45 % Favored : 86.07 % 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: -0.33 (0.27), residues: 951 helix: 0.65 (0.23), residues: 549 sheet: -1.27 (0.60), residues: 63 loop : -1.38 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 693 TYR 0.013 0.001 TYR A 646 PHE 0.021 0.001 PHE A1124 TRP 0.013 0.001 TRP A 960 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7838) covalent geometry : angle 0.57839 / 0.28 (10692) SS BOND : bond 0.00851 / 0.33 ( 6) SS BOND : angle 1.69785 / 0.96 ( 12) hydrogen bonds : bond 0.04193 / 2.81 ( 412) hydrogen bonds : angle 4.33729 / 2.92 ( 1188) link_BETA1-4 : bond 0.00805 / 0.39 ( 3) link_BETA1-4 : angle 1.50619 / 0.84 ( 9) link_NAG-ASN : bond 0.00432 / 0.20 ( 7) link_NAG-ASN : angle 3.68869 / 3.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.208 Fit side-chains REVERT: A 351 TRP cc_start: 0.7541 (m100) cc_final: 0.7268 (m-10) REVERT: A 560 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8270 (mtpt) REVERT: A 616 MET cc_start: 0.8451 (ppp) cc_final: 0.7921 (ttt) REVERT: A 657 TRP cc_start: 0.6479 (OUTLIER) cc_final: 0.5116 (t60) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 0.0529 time to fit residues: 7.3282 Evaluate side-chains 81 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1047 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 GLN A 926 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105713 restraints weight = 9148.472| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.42 r_work: 0.2984 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 0.003 0.045 7854 Z= 0.122 Angle : 0.565 9.441 10734 Z= 0.266 Chirality : 0.040 0.292 1274 Planarity : 0.003 0.032 1321 Dihedral : 6.121 70.638 1059 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.60 % Allowed : 13.32 % Favored : 85.08 % 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: 0.00 (0.28), residues: 951 helix: 0.86 (0.23), residues: 547 sheet: -0.80 (0.62), residues: 64 loop : -1.18 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.013 0.001 TYR A 646 PHE 0.021 0.001 PHE A1124 TRP 0.012 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7838) covalent geometry : angle 0.54686 / 0.26 (10692) SS BOND : bond 0.00298 / 0.14 ( 6) SS BOND : angle 0.83374 / 0.50 ( 12) hydrogen bonds : bond 0.03907 / 2.63 ( 412) hydrogen bonds : angle 4.22650 / 2.84 ( 1188) link_BETA1-4 : bond 0.00667 / 0.33 ( 3) link_BETA1-4 : angle 1.64093 / 0.91 ( 9) link_NAG-ASN : bond 0.00466 / 0.21 ( 7) link_NAG-ASN : angle 3.04816 / 2.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.214 Fit side-chains REVERT: A 351 TRP cc_start: 0.7547 (m100) cc_final: 0.7250 (m-10) REVERT: A 616 MET cc_start: 0.8412 (ppp) cc_final: 0.7993 (ttt) REVERT: A 626 ASN cc_start: 0.8498 (m110) cc_final: 0.8167 (m-40) REVERT: A 657 TRP cc_start: 0.6364 (OUTLIER) cc_final: 0.4968 (t60) REVERT: A 1203 GLU cc_start: 0.7625 (tt0) cc_final: 0.7384 (tt0) outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.0518 time to fit residues: 7.9966 Evaluate side-chains 86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101104 restraints weight = 9253.432| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.43 r_work: 0.2928 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7854 Z= 0.201 Angle : 0.622 9.496 10734 Z= 0.293 Chirality : 0.043 0.289 1274 Planarity : 0.004 0.034 1321 Dihedral : 6.135 67.026 1059 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.85 % Allowed : 14.18 % Favored : 83.97 % 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: -0.17 (0.27), residues: 951 helix: 0.73 (0.23), residues: 546 sheet: -0.87 (0.58), residues: 74 loop : -1.26 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1081 TYR 0.012 0.001 TYR A 646 PHE 0.022 0.002 PHE A1124 TRP 0.013 0.001 TRP A 960 HIS 0.005 0.001 HIS A 842 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 ( 7838) covalent geometry : angle 0.60178 / 0.29 (10692) SS BOND : bond 0.00439 / 0.23 ( 6) SS BOND : angle 0.94001 / 0.59 ( 12) hydrogen bonds : bond 0.04321 / 2.88 ( 412) hydrogen bonds : angle 4.32372 / 2.91 ( 1188) link_BETA1-4 : bond 0.00603 / 0.29 ( 3) link_BETA1-4 : angle 1.82251 / 1.04 ( 9) link_NAG-ASN : bond 0.00474 / 0.21 ( 7) link_NAG-ASN : angle 3.41743 / 2.89 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.262 Fit side-chains REVERT: A 351 TRP cc_start: 0.7614 (m100) cc_final: 0.7332 (m-10) REVERT: A 534 ASP cc_start: 0.6932 (t0) cc_final: 0.6721 (t0) REVERT: A 616 MET cc_start: 0.8472 (ppp) cc_final: 0.8025 (ttt) REVERT: A 626 ASN cc_start: 0.8548 (m110) cc_final: 0.8231 (m-40) REVERT: A 657 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.4913 (t60) REVERT: A 814 LYS cc_start: 0.4595 (mmtt) cc_final: 0.3892 (tptp) REVERT: A 1203 GLU cc_start: 0.7660 (tt0) cc_final: 0.7451 (tt0) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.0546 time to fit residues: 7.7124 Evaluate side-chains 86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 0.0060 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.127136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103974 restraints weight = 9150.769| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.42 r_work: 0.2969 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.128 Angle : 0.572 9.530 10734 Z= 0.266 Chirality : 0.040 0.286 1274 Planarity : 0.003 0.032 1321 Dihedral : 5.887 61.424 1059 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.11 % Allowed : 15.66 % Favored : 83.23 % 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: 0.11 (0.28), residues: 951 helix: 0.91 (0.23), residues: 548 sheet: -0.67 (0.59), residues: 74 loop : -1.09 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 693 TYR 0.013 0.001 TYR A 646 PHE 0.022 0.001 PHE A1124 TRP 0.013 0.001 TRP A 960 HIS 0.003 0.001 HIS A 842 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7838) covalent geometry : angle 0.54458 / 0.26 (10692) SS BOND : bond 0.00286 / 0.15 ( 6) SS BOND : angle 0.70438 / 0.43 ( 12) hydrogen bonds : bond 0.03887 / 2.61 ( 412) hydrogen bonds : angle 4.23669 / 2.85 ( 1188) link_BETA1-4 : bond 0.00624 / 0.31 ( 3) link_BETA1-4 : angle 1.48556 / 0.88 ( 9) link_NAG-ASN : bond 0.00469 / 0.21 ( 7) link_NAG-ASN : angle 3.84682 / 3.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.314 Fit side-chains REVERT: A 351 TRP cc_start: 0.7575 (m100) cc_final: 0.7268 (m-10) REVERT: A 407 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 560 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8337 (mtpt) REVERT: A 616 MET cc_start: 0.8407 (ppp) cc_final: 0.7800 (ttt) REVERT: A 626 ASN cc_start: 0.8485 (m110) cc_final: 0.8134 (m-40) REVERT: A 657 TRP cc_start: 0.6165 (OUTLIER) cc_final: 0.4735 (t60) REVERT: A 814 LYS cc_start: 0.4599 (mmtt) cc_final: 0.3934 (tptp) REVERT: A 1203 GLU cc_start: 0.7627 (tt0) cc_final: 0.7397 (tt0) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.0534 time to fit residues: 7.8741 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103328 restraints weight = 9164.462| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.42 r_work: 0.2962 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7854 Z= 0.148 Angle : 0.597 9.615 10734 Z= 0.279 Chirality : 0.042 0.285 1274 Planarity : 0.004 0.032 1321 Dihedral : 5.787 56.894 1058 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.85 % Allowed : 15.41 % Favored : 82.74 % 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: 0.15 (0.28), residues: 951 helix: 0.91 (0.23), residues: 547 sheet: -0.51 (0.59), residues: 74 loop : -1.05 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 693 TYR 0.013 0.001 TYR A 646 PHE 0.023 0.001 PHE A1124 TRP 0.012 0.001 TRP A 960 HIS 0.004 0.001 HIS A 842 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7838) covalent geometry : angle 0.56498 / 0.27 (10692) SS BOND : bond 0.00329 / 0.17 ( 6) SS BOND : angle 0.74584 / 0.46 ( 12) hydrogen bonds : bond 0.04033 / 2.68 ( 412) hydrogen bonds : angle 4.20961 / 2.83 ( 1188) link_BETA1-4 : bond 0.00553 / 0.26 ( 3) link_BETA1-4 : angle 1.29759 / 0.77 ( 9) link_NAG-ASN : bond 0.00475 / 0.21 ( 7) link_NAG-ASN : angle 4.32604 / 3.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.208 Fit side-chains REVERT: A 351 TRP cc_start: 0.7586 (m100) cc_final: 0.7277 (m-10) REVERT: A 407 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 560 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8312 (mtpt) REVERT: A 616 MET cc_start: 0.8366 (ppp) cc_final: 0.7773 (ttt) REVERT: A 626 ASN cc_start: 0.8494 (m110) cc_final: 0.8143 (m-40) REVERT: A 657 TRP cc_start: 0.6113 (OUTLIER) cc_final: 0.4658 (t60) REVERT: A 814 LYS cc_start: 0.4607 (mmtt) cc_final: 0.4016 (tptp) REVERT: A 1203 GLU cc_start: 0.7656 (tt0) cc_final: 0.7423 (tt0) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.0566 time to fit residues: 8.1209 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 58 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106691 restraints weight = 9079.290| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.41 r_work: 0.2999 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7854 Z= 0.109 Angle : 0.582 15.683 10734 Z= 0.266 Chirality : 0.040 0.279 1274 Planarity : 0.003 0.030 1321 Dihedral : 5.644 57.102 1058 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.60 % Allowed : 15.66 % Favored : 82.74 % 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: 0.46 (0.28), residues: 951 helix: 1.17 (0.23), residues: 542 sheet: -0.27 (0.61), residues: 74 loop : -0.94 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 498 TYR 0.013 0.001 TYR A 646 PHE 0.023 0.001 PHE A1124 TRP 0.013 0.001 TRP A 960 HIS 0.002 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7838) covalent geometry : angle 0.53331 / 0.25 (10692) SS BOND : bond 0.00211 / 0.12 ( 6) SS BOND : angle 0.54018 / 0.34 ( 12) hydrogen bonds : bond 0.03673 / 2.45 ( 412) hydrogen bonds : angle 4.12285 / 2.77 ( 1188) link_BETA1-4 : bond 0.00559 / 0.27 ( 3) link_BETA1-4 : angle 1.35604 / 0.82 ( 9) link_NAG-ASN : bond 0.00458 / 0.22 ( 7) link_NAG-ASN : angle 5.23890 / 4.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.270 Fit side-chains REVERT: A 351 TRP cc_start: 0.7629 (m100) cc_final: 0.7333 (m-10) REVERT: A 407 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 607 MET cc_start: 0.8160 (mmm) cc_final: 0.7920 (mtp) REVERT: A 616 MET cc_start: 0.8419 (ppp) cc_final: 0.7851 (ttt) REVERT: A 626 ASN cc_start: 0.8551 (m110) cc_final: 0.8231 (m-40) REVERT: A 657 TRP cc_start: 0.6059 (OUTLIER) cc_final: 0.4704 (t60) REVERT: A 788 MET cc_start: 0.7896 (mmp) cc_final: 0.7681 (mmp) REVERT: A 814 LYS cc_start: 0.4661 (mmtt) cc_final: 0.4055 (tptp) REVERT: A 851 LEU cc_start: 0.7862 (tt) cc_final: 0.6818 (mm) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.0549 time to fit residues: 8.1602 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.0000 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 GLN A1009 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106402 restraints weight = 9086.715| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.41 r_work: 0.2989 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.130 Angle : 0.612 18.684 10734 Z= 0.278 Chirality : 0.043 0.522 1274 Planarity : 0.003 0.031 1321 Dihedral : 5.626 57.073 1058 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.48 % Allowed : 15.78 % Favored : 82.74 % 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: 0.44 (0.28), residues: 951 helix: 1.09 (0.23), residues: 548 sheet: -0.13 (0.62), residues: 74 loop : -0.88 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 498 TYR 0.012 0.001 TYR A 646 PHE 0.023 0.001 PHE A1124 TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS A1009 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7838) covalent geometry : angle 0.56144 / 0.27 (10692) SS BOND : bond 0.00263 / 0.14 ( 6) SS BOND : angle 0.62334 / 0.39 ( 12) hydrogen bonds : bond 0.03787 / 2.53 ( 412) hydrogen bonds : angle 4.10854 / 2.76 ( 1188) link_BETA1-4 : bond 0.00679 / 0.35 ( 3) link_BETA1-4 : angle 1.10555 / 0.63 ( 9) link_NAG-ASN : bond 0.00493 / 0.22 ( 7) link_NAG-ASN : angle 5.50774 / 4.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.188 Fit side-chains REVERT: A 351 TRP cc_start: 0.7602 (m100) cc_final: 0.7299 (m-10) REVERT: A 407 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 607 MET cc_start: 0.8214 (mmm) cc_final: 0.7955 (mtp) REVERT: A 616 MET cc_start: 0.8366 (ppp) cc_final: 0.7790 (ttt) REVERT: A 626 ASN cc_start: 0.8509 (m110) cc_final: 0.8168 (m-40) REVERT: A 657 TRP cc_start: 0.6065 (OUTLIER) cc_final: 0.4732 (t60) REVERT: A 814 LYS cc_start: 0.4537 (mmtt) cc_final: 0.4017 (tptp) REVERT: A 1104 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: A 1208 MET cc_start: 0.8645 (tpp) cc_final: 0.8180 (tpt) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.0492 time to fit residues: 6.8847 Evaluate side-chains 89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.105568 restraints weight = 9152.277| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.41 r_work: 0.2988 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.129 Angle : 0.587 13.986 10734 Z= 0.271 Chirality : 0.042 0.357 1274 Planarity : 0.003 0.031 1321 Dihedral : 5.549 57.085 1058 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.60 % Allowed : 15.66 % Favored : 82.74 % 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: 0.48 (0.28), residues: 951 helix: 1.16 (0.23), residues: 542 sheet: -0.00 (0.64), residues: 74 loop : -0.94 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 498 TYR 0.012 0.001 TYR A 646 PHE 0.024 0.001 PHE A1124 TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS A1009 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7838) covalent geometry : angle 0.55162 / 0.26 (10692) SS BOND : bond 0.00268 / 0.14 ( 6) SS BOND : angle 0.65317 / 0.40 ( 12) hydrogen bonds : bond 0.03801 / 2.53 ( 412) hydrogen bonds : angle 4.12219 / 2.77 ( 1188) link_BETA1-4 : bond 0.00882 / 0.45 ( 3) link_BETA1-4 : angle 0.87554 / 0.49 ( 9) link_NAG-ASN : bond 0.00427 / 0.19 ( 7) link_NAG-ASN : angle 4.57101 / 3.94 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.282 Fit side-chains REVERT: A 351 TRP cc_start: 0.7595 (m100) cc_final: 0.7290 (m-10) REVERT: A 407 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 607 MET cc_start: 0.8199 (mmm) cc_final: 0.7944 (mtp) REVERT: A 616 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7792 (ttt) REVERT: A 626 ASN cc_start: 0.8483 (m110) cc_final: 0.8155 (m-40) REVERT: A 657 TRP cc_start: 0.6044 (OUTLIER) cc_final: 0.4807 (t60) REVERT: A 814 LYS cc_start: 0.4470 (mmtt) cc_final: 0.4067 (tptp) REVERT: A 1104 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8375 (pt0) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.0538 time to fit residues: 7.7822 Evaluate side-chains 91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 61 optimal weight: 0.0060 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.106314 restraints weight = 9065.908| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.41 r_work: 0.3005 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7854 Z= 0.107 Angle : 0.575 12.804 10734 Z= 0.265 Chirality : 0.041 0.324 1274 Planarity : 0.003 0.030 1321 Dihedral : 5.467 57.300 1058 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.60 % Allowed : 16.28 % Favored : 82.12 % 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: 0.63 (0.28), residues: 951 helix: 1.28 (0.23), residues: 543 sheet: 0.05 (0.63), residues: 74 loop : -0.86 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.014 0.001 TYR A 646 PHE 0.023 0.001 PHE A1124 TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS A1009 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7838) covalent geometry : angle 0.53450 / 0.26 (10692) SS BOND : bond 0.00205 / 0.11 ( 6) SS BOND : angle 0.53561 / 0.33 ( 12) hydrogen bonds : bond 0.03627 / 2.42 ( 412) hydrogen bonds : angle 4.05787 / 2.72 ( 1188) link_BETA1-4 : bond 0.00759 / 0.38 ( 3) link_BETA1-4 : angle 0.89859 / 0.51 ( 9) link_NAG-ASN : bond 0.00325 / 0.13 ( 7) link_NAG-ASN : angle 4.80504 / 4.29 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1668.80 seconds wall clock time: 29 minutes 15.33 seconds (1755.33 seconds total)