Starting phenix.real_space_refine on Sat Jul 4 00:44:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m5y_23685/07_2026/7m5y_23685_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m5y_23685/07_2026/7m5y_23685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m5y_23685/07_2026/7m5y_23685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m5y_23685/07_2026/7m5y_23685.map" model { file = "/net/cci-nas-00/data/ceres_data/7m5y_23685/07_2026/7m5y_23685_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m5y_23685/07_2026/7m5y_23685_trim.cif" } resolution = 3.0 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= 0.002 sd= 0.023 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 5202 2.51 5 N 1267 2.21 5 O 1385 1.98 5 F 4 1.80 5 H 7534 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 15447 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 14990 Classifications: {'peptide': 1000} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 930} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 14, 'TRP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "A" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 457 Unusual residues: {' MG': 1, 'C14': 1, 'CLR': 4, 'D10': 9, 'D12': 1, 'EUJ': 1, 'LMT': 1, 'MF4': 1, 'NAG': 1, 'SPK': 1, 'Y01': 3} Classifications: {'undetermined': 24, 'water': 8} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.28, per 1000 atoms: 0.15 Number of scatterers: 15447 At special positions: 0 Unit cell: (77.19, 95.45, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 50 16.00 P 3 15.00 Mg 2 11.99 F 4 9.00 O 1385 8.00 N 1267 7.00 C 5202 6.00 H 7534 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 NAG-ASN " NAG A1222 " - " ASN A1033 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 416.9 milliseconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 50.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.505A pdb=" N ALA A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.620A pdb=" N SER A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.604A pdb=" N GLY A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 290 removed outlier: 3.664A pdb=" N ALA A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.999A pdb=" N LYS A 427 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 428 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 Processing helix chain 'A' and resid 453 through 469 removed outlier: 4.101A pdb=" N VAL A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 4.491A pdb=" N CYS A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.774A pdb=" N GLY A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 506' Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.587A pdb=" N ARG A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 826 through 837 Processing helix chain 'A' and resid 840 through 847 removed outlier: 3.540A pdb=" N GLN A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 869 removed outlier: 3.724A pdb=" N THR A 860 " --> pdb=" O PRO A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 889 Processing helix chain 'A' and resid 914 through 953 removed outlier: 3.693A pdb=" N MET A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 968 Processing helix chain 'A' and resid 968 through 978 Processing helix chain 'A' and resid 998 through 1024 Processing helix chain 'A' and resid 1038 through 1042 removed outlier: 3.504A pdb=" N LEU A1042 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1066 removed outlier: 3.547A pdb=" N PHE A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1098 Processing helix chain 'A' and resid 1113 through 1149 Proline residue: A1143 - end of helix Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 110 removed outlier: 5.234A pdb=" N ARG A 164 " --> pdb=" O TRP A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 320 removed outlier: 4.703A pdb=" N VAL A 391 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 392 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A 330 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.612A pdb=" N MET A 339 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA A 383 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU A 337 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 495 removed outlier: 7.166A pdb=" N VAL A 873 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE A 893 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A 875 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 509 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 849 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A 849 " --> pdb=" O ARG A 821 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 823 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 851 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A 825 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS A 772 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA A 824 " --> pdb=" O HIS A 772 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 774 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 530 removed outlier: 6.665A pdb=" N VAL A 723 " --> pdb=" O MET A 526 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 528 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 721 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU A 719 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 690 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 721 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 688 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 723 " --> pdb=" O ARG A 686 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 686 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 638 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG A 627 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 640 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA A 601 " --> pdb=" O VAL A 624 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1203 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: 3.13 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7508 1.03 - 1.23: 30 1.23 - 1.42: 3028 1.42 - 1.62: 4951 1.62 - 1.82: 78 Bond restraints: 15595 Sorted by residual: bond pdb=" O3 EUJ A1224 " pdb=" P3 EUJ A1224 " ideal model delta sigma weight residual 1.727 1.574 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" CAI Y01 A1203 " pdb=" CAK Y01 A1203 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" CAI Y01 A1208 " pdb=" CAK Y01 A1208 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG A1222 " pdb=" C2 NAG A1222 " ideal model delta sigma weight residual 1.532 1.614 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CAI Y01 A1205 " pdb=" CAK Y01 A1205 " ideal model delta sigma weight residual 1.492 1.411 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 15590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 27392 2.49 - 4.98: 595 4.98 - 7.47: 86 7.47 - 9.96: 17 9.96 - 12.45: 8 Bond angle restraints: 28098 Sorted by residual: angle pdb=" CB ARG A 725 " pdb=" CG ARG A 725 " pdb=" CD ARG A 725 " ideal model delta sigma weight residual 111.30 123.64 -12.34 2.30e+00 1.89e-01 2.88e+01 angle pdb=" N GLU A1165 " pdb=" CA GLU A1165 " pdb=" CB GLU A1165 " ideal model delta sigma weight residual 110.12 116.52 -6.40 1.47e+00 4.63e-01 1.89e+01 angle pdb=" CAM Y01 A1208 " pdb=" CAY Y01 A1208 " pdb=" OAW Y01 A1208 " ideal model delta sigma weight residual 111.19 123.64 -12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" OAG Y01 A1208 " pdb=" CAY Y01 A1208 " pdb=" OAW Y01 A1208 " ideal model delta sigma weight residual 123.38 111.45 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CAM Y01 A1205 " pdb=" CAY Y01 A1205 " pdb=" OAW Y01 A1205 " ideal model delta sigma weight residual 111.19 122.55 -11.36 3.00e+00 1.11e-01 1.43e+01 ... (remaining 28093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.96: 7509 30.96 - 61.92: 306 61.92 - 92.87: 45 92.87 - 123.83: 12 123.83 - 154.79: 1 Dihedral angle restraints: 7873 sinusoidal: 4607 harmonic: 3266 Sorted by residual: dihedral pdb=" C1 EUJ A1224 " pdb=" O1 EUJ A1224 " pdb=" P1 EUJ A1224 " pdb=" O11 EUJ A1224 " ideal model delta sinusoidal sigma weight residual 50.66 -104.13 154.79 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA THR A 750 " pdb=" C THR A 750 " pdb=" N GLY A 751 " pdb=" CA GLY A 751 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C10 CLR A1206 " pdb=" C1 CLR A1206 " pdb=" C2 CLR A1206 " pdb=" C3 CLR A1206 " ideal model delta sinusoidal sigma weight residual -56.83 64.53 -121.36 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 7870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.970: 1348 0.970 - 1.939: 0 1.939 - 2.909: 0 2.909 - 3.878: 0 3.878 - 4.848: 1 Chirality restraints: 1349 Sorted by residual: chirality pdb=" C4 EUJ A1224 " pdb=" C3 EUJ A1224 " pdb=" C5 EUJ A1224 " pdb=" O4 EUJ A1224 " both_signs ideal model delta sigma weight residual False 2.45 -2.40 4.85 2.00e-01 2.50e+01 5.88e+02 chirality pdb=" C2 NAG A1222 " pdb=" C1 NAG A1222 " pdb=" C3 NAG A1222 " pdb=" N2 NAG A1222 " both_signs ideal model delta sigma weight residual False -2.49 -2.87 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C1' LMT A1204 " pdb=" C2' LMT A1204 " pdb=" O1' LMT A1204 " pdb=" O5' LMT A1204 " both_signs ideal model delta sigma weight residual False 2.31 2.67 -0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1346 not shown) Planarity restraints: 2237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 926 " -0.034 2.00e-02 2.50e+03 6.83e-02 4.67e+01 pdb=" C SER A 926 " 0.118 2.00e-02 2.50e+03 pdb=" O SER A 926 " -0.044 2.00e-02 2.50e+03 pdb=" N LEU A 927 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 676 " -0.023 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C MET A 676 " 0.080 2.00e-02 2.50e+03 pdb=" O MET A 676 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A 677 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 772 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C HIS A 772 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS A 772 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 773 " 0.024 2.00e-02 2.50e+03 ... (remaining 2234 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2493 2.28 - 2.86: 33956 2.86 - 3.44: 39620 3.44 - 4.02: 52365 4.02 - 4.60: 80860 Nonbonded interactions: 209294 Sorted by model distance: nonbonded pdb=" OD1 ASN A 219 " pdb=" HG1 THR A 398 " model vdw 1.704 2.450 nonbonded pdb=" HE ARG A 460 " pdb=" OH TYR A 952 " model vdw 1.723 2.450 nonbonded pdb=" O MET A 676 " pdb=" HG SER A 679 " model vdw 1.728 2.450 nonbonded pdb=" OE1 GLU A 658 " pdb=" H GLU A 658 " model vdw 1.730 2.450 nonbonded pdb=" O LEU A1087 " pdb=" HG SER A1090 " model vdw 1.735 2.450 ... (remaining 209289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.070 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.040 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 8062 Z= 0.346 Angle : 1.191 12.446 10984 Z= 0.576 Chirality : 0.144 4.848 1349 Planarity : 0.007 0.091 1316 Dihedral : 16.709 154.791 3434 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.03 (0.27), residues: 976 helix: 1.31 (0.24), residues: 455 sheet: -1.35 (0.40), residues: 157 loop : -0.92 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 989 TYR 0.015 0.002 TYR A 680 PHE 0.015 0.002 PHE A 945 TRP 0.033 0.002 TRP A 258 HIS 0.010 0.002 HIS A 772 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.35 ( 8061) covalent geometry : angle 1.19061 / 0.58 (10981) hydrogen bonds : bond 0.15196 / 10.57 ( 421) hydrogen bonds : angle 6.64409 / 4.70 ( 1203) link_NAG-ASN : bond 0.00694 / 0.37 ( 1) link_NAG-ASN : angle 2.27809 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.5982 (ttt) cc_final: 0.5750 (tmm) REVERT: A 968 LEU cc_start: 0.8927 (mt) cc_final: 0.8692 (mt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.5262 time to fit residues: 47.1531 Evaluate side-chains 49 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.070518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060015 restraints weight = 100336.006| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.37 r_work: 0.3109 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8062 Z= 0.131 Angle : 0.609 7.167 10984 Z= 0.291 Chirality : 0.042 0.221 1349 Planarity : 0.005 0.054 1316 Dihedral : 13.526 163.065 1780 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.88 % Allowed : 7.43 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.55 (0.27), residues: 976 helix: 1.75 (0.24), residues: 461 sheet: -1.13 (0.39), residues: 157 loop : -0.70 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 725 TYR 0.015 0.001 TYR A 936 PHE 0.012 0.001 PHE A1159 TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS A 772 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8061) covalent geometry : angle 0.60769 / 0.29 (10981) hydrogen bonds : bond 0.04164 / 2.82 ( 421) hydrogen bonds : angle 4.98101 / 3.58 ( 1203) link_NAG-ASN : bond 0.00639 / 0.34 ( 1) link_NAG-ASN : angle 2.61558 / 1.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.5651 (ttt) cc_final: 0.4884 (tmm) REVERT: A 865 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: A 899 GLU cc_start: 0.8656 (tp30) cc_final: 0.8418 (tp30) outliers start: 7 outliers final: 0 residues processed: 53 average time/residue: 0.6451 time to fit residues: 37.7357 Evaluate side-chains 47 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 865 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.9928 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.069599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058901 restraints weight = 101436.661| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.43 r_work: 0.3099 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8062 Z= 0.121 Angle : 0.553 6.735 10984 Z= 0.264 Chirality : 0.041 0.216 1349 Planarity : 0.004 0.035 1316 Dihedral : 11.758 170.145 1780 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.13 % Allowed : 8.06 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.87 (0.28), residues: 976 helix: 2.04 (0.24), residues: 463 sheet: -0.87 (0.39), residues: 162 loop : -0.63 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 725 TYR 0.012 0.001 TYR A 936 PHE 0.011 0.001 PHE A1159 TRP 0.007 0.001 TRP A 258 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8061) covalent geometry : angle 0.55175 / 0.26 (10981) hydrogen bonds : bond 0.03489 / 2.33 ( 421) hydrogen bonds : angle 4.49450 / 3.22 ( 1203) link_NAG-ASN : bond 0.00683 / 0.36 ( 1) link_NAG-ASN : angle 2.59664 / 1.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.9104 (ttt) cc_final: 0.8813 (ttt) REVERT: A 637 MET cc_start: 0.5876 (ttt) cc_final: 0.5031 (tmm) REVERT: A 899 GLU cc_start: 0.8812 (tp30) cc_final: 0.8357 (mm-30) REVERT: A 926 SER cc_start: 0.9394 (m) cc_final: 0.9094 (p) outliers start: 9 outliers final: 2 residues processed: 52 average time/residue: 0.8051 time to fit residues: 46.3610 Evaluate side-chains 50 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 946 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.069054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058469 restraints weight = 101266.950| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.44 r_work: 0.3080 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8062 Z= 0.140 Angle : 0.542 7.647 10984 Z= 0.260 Chirality : 0.040 0.210 1349 Planarity : 0.004 0.038 1316 Dihedral : 10.811 172.548 1780 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.51 % Allowed : 8.82 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.98 (0.28), residues: 976 helix: 2.14 (0.24), residues: 469 sheet: -0.89 (0.39), residues: 159 loop : -0.62 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 725 TYR 0.014 0.001 TYR A 936 PHE 0.009 0.001 PHE A 945 TRP 0.007 0.001 TRP A 258 HIS 0.002 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8061) covalent geometry : angle 0.54047 / 0.26 (10981) hydrogen bonds : bond 0.03256 / 2.16 ( 421) hydrogen bonds : angle 4.35604 / 3.12 ( 1203) link_NAG-ASN : bond 0.00479 / 0.25 ( 1) link_NAG-ASN : angle 2.66942 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.9165 (ttt) cc_final: 0.8919 (ttt) REVERT: A 637 MET cc_start: 0.5886 (ttt) cc_final: 0.5002 (tmm) REVERT: A 865 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8606 (mp0) outliers start: 12 outliers final: 2 residues processed: 55 average time/residue: 0.7843 time to fit residues: 47.8680 Evaluate side-chains 51 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 946 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.068774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057638 restraints weight = 102095.554| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.66 r_work: 0.3119 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8062 Z= 0.152 Angle : 0.547 6.714 10984 Z= 0.263 Chirality : 0.040 0.204 1349 Planarity : 0.004 0.032 1316 Dihedral : 9.741 154.312 1780 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.88 % Allowed : 10.08 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.12 (0.28), residues: 976 helix: 2.29 (0.24), residues: 470 sheet: -0.75 (0.40), residues: 157 loop : -0.67 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 725 TYR 0.014 0.001 TYR A 936 PHE 0.014 0.001 PHE A 536 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 8061) covalent geometry : angle 0.54500 / 0.26 (10981) hydrogen bonds : bond 0.03231 / 2.16 ( 421) hydrogen bonds : angle 4.24285 / 3.05 ( 1203) link_NAG-ASN : bond 0.00449 / 0.24 ( 1) link_NAG-ASN : angle 3.06181 / 1.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.5804 (ttt) cc_final: 0.4851 (tmm) REVERT: A 865 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: A 899 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 926 SER cc_start: 0.9311 (m) cc_final: 0.8973 (p) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.7127 time to fit residues: 42.6622 Evaluate side-chains 52 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 946 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.069575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.058753 restraints weight = 100613.198| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.54 r_work: 0.3098 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8062 Z= 0.115 Angle : 0.520 7.299 10984 Z= 0.248 Chirality : 0.040 0.207 1349 Planarity : 0.004 0.031 1316 Dihedral : 9.179 149.981 1780 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.63 % Allowed : 10.71 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.27 (0.28), residues: 976 helix: 2.43 (0.24), residues: 470 sheet: -0.59 (0.40), residues: 157 loop : -0.68 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.012 0.001 TYR A 936 PHE 0.009 0.001 PHE A1132 TRP 0.006 0.001 TRP A 258 HIS 0.001 0.000 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8061) covalent geometry : angle 0.51680 / 0.25 (10981) hydrogen bonds : bond 0.03050 / 2.03 ( 421) hydrogen bonds : angle 4.11927 / 2.95 ( 1203) link_NAG-ASN : bond 0.00452 / 0.24 ( 1) link_NAG-ASN : angle 3.29485 / 1.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 637 MET cc_start: 0.5932 (ttt) cc_final: 0.5582 (tmm) REVERT: A 865 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: A 899 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8054 (mm-30) REVERT: A 926 SER cc_start: 0.9367 (m) cc_final: 0.9035 (p) REVERT: A 1013 THR cc_start: 0.9414 (m) cc_final: 0.9209 (t) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.6379 time to fit residues: 38.7876 Evaluate side-chains 52 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 946 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 20 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.068566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057885 restraints weight = 100647.812| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.47 r_work: 0.3055 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8062 Z= 0.206 Angle : 0.575 7.616 10984 Z= 0.279 Chirality : 0.041 0.182 1349 Planarity : 0.004 0.028 1316 Dihedral : 8.978 151.020 1780 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.13 % Allowed : 10.45 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.20 (0.28), residues: 976 helix: 2.43 (0.24), residues: 468 sheet: -0.66 (0.40), residues: 168 loop : -0.75 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.013 0.001 TYR A 936 PHE 0.010 0.001 PHE A 945 TRP 0.008 0.001 TRP A 258 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 8061) covalent geometry : angle 0.57172 / 0.28 (10981) hydrogen bonds : bond 0.03320 / 2.22 ( 421) hydrogen bonds : angle 4.25942 / 3.06 ( 1203) link_NAG-ASN : bond 0.00293 / 0.15 ( 1) link_NAG-ASN : angle 3.76599 / 2.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.6142 (ttt) cc_final: 0.5807 (tmm) REVERT: A 790 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8254 (pp20) REVERT: A 865 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: A 899 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 926 SER cc_start: 0.9404 (m) cc_final: 0.9105 (p) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 0.6773 time to fit residues: 41.2572 Evaluate side-chains 53 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 946 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.0370 chunk 2 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.057945 restraints weight = 101191.076| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.51 r_work: 0.3072 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8062 Z= 0.153 Angle : 0.548 7.736 10984 Z= 0.262 Chirality : 0.040 0.166 1349 Planarity : 0.004 0.030 1316 Dihedral : 8.730 152.515 1780 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.01 % Allowed : 10.83 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.23 (0.28), residues: 976 helix: 2.41 (0.24), residues: 474 sheet: -0.57 (0.40), residues: 162 loop : -0.77 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 725 TYR 0.013 0.001 TYR A 936 PHE 0.010 0.001 PHE A 945 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8061) covalent geometry : angle 0.54353 / 0.26 (10981) hydrogen bonds : bond 0.03188 / 2.12 ( 421) hydrogen bonds : angle 4.17775 / 3.00 ( 1203) link_NAG-ASN : bond 0.00345 / 0.18 ( 1) link_NAG-ASN : angle 4.13531 / 2.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.6002 (ttt) cc_final: 0.5655 (tmm) REVERT: A 790 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8235 (pp20) REVERT: A 865 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: A 926 SER cc_start: 0.9342 (m) cc_final: 0.9031 (p) REVERT: A 940 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8804 (t80) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.7731 time to fit residues: 46.1406 Evaluate side-chains 55 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1007 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.068360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057317 restraints weight = 100945.101| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.58 r_work: 0.3057 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8062 Z= 0.116 Angle : 0.537 7.385 10984 Z= 0.253 Chirality : 0.040 0.145 1349 Planarity : 0.004 0.031 1316 Dihedral : 8.462 154.128 1780 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.76 % Allowed : 11.34 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.35 (0.28), residues: 976 helix: 2.48 (0.24), residues: 474 sheet: -0.45 (0.40), residues: 162 loop : -0.70 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.012 0.001 TYR A 936 PHE 0.009 0.001 PHE A 945 TRP 0.006 0.001 TRP A 258 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8061) covalent geometry : angle 0.53134 / 0.25 (10981) hydrogen bonds : bond 0.03057 / 2.04 ( 421) hydrogen bonds : angle 4.08687 / 2.93 ( 1203) link_NAG-ASN : bond 0.00406 / 0.21 ( 1) link_NAG-ASN : angle 4.58677 / 2.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 637 MET cc_start: 0.6094 (ttt) cc_final: 0.5813 (tmm) REVERT: A 790 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8280 (pp20) REVERT: A 865 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: A 926 SER cc_start: 0.9398 (m) cc_final: 0.9096 (p) REVERT: A 940 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8852 (t80) outliers start: 6 outliers final: 1 residues processed: 51 average time/residue: 0.7828 time to fit residues: 44.0866 Evaluate side-chains 50 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 940 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.068378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057305 restraints weight = 101587.307| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.60 r_work: 0.3078 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8062 Z= 0.116 Angle : 0.534 6.773 10984 Z= 0.252 Chirality : 0.039 0.143 1349 Planarity : 0.004 0.031 1316 Dihedral : 8.258 155.427 1780 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.76 % Allowed : 11.34 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.39 (0.28), residues: 976 helix: 2.50 (0.24), residues: 477 sheet: -0.47 (0.41), residues: 157 loop : -0.65 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.012 0.001 TYR A 936 PHE 0.008 0.001 PHE A 945 TRP 0.006 0.001 TRP A 258 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8061) covalent geometry : angle 0.52778 / 0.25 (10981) hydrogen bonds : bond 0.02974 / 1.99 ( 421) hydrogen bonds : angle 4.04507 / 2.90 ( 1203) link_NAG-ASN : bond 0.00517 / 0.27 ( 1) link_NAG-ASN : angle 5.01042 / 2.81 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue LYS 427 is missing expected H atoms. Skipping. Residue LEU 432 is missing expected H atoms. Skipping. Residue LYS 1152 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.6079 (ttt) cc_final: 0.5757 (tmm) REVERT: A 790 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8264 (pp20) REVERT: A 865 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8579 (mp0) REVERT: A 926 SER cc_start: 0.9393 (m) cc_final: 0.9089 (p) REVERT: A 940 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8874 (t80) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.7806 time to fit residues: 44.0641 Evaluate side-chains 53 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 940 TYR Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1007 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.067753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057036 restraints weight = 101282.626| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.45 r_work: 0.3053 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8062 Z= 0.203 Angle : 0.573 7.246 10984 Z= 0.277 Chirality : 0.040 0.150 1349 Planarity : 0.004 0.027 1316 Dihedral : 8.404 156.615 1780 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.88 % Allowed : 11.21 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.26 (0.28), residues: 976 helix: 2.42 (0.24), residues: 478 sheet: -0.57 (0.40), residues: 163 loop : -0.78 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 725 TYR 0.013 0.001 TYR A 936 PHE 0.014 0.001 PHE A 945 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 8061) covalent geometry : angle 0.56626 / 0.28 (10981) hydrogen bonds : bond 0.03258 / 2.19 ( 421) hydrogen bonds : angle 4.20055 / 3.01 ( 1203) link_NAG-ASN : bond 0.00489 / 0.26 ( 1) link_NAG-ASN : angle 5.29775 / 2.99 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.90 seconds wall clock time: 61 minutes 23.26 seconds (3683.26 seconds total)