Starting phenix.real_space_refine on Thu Jul 2 07:08:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.map" model { file = "/net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2h_30957/07_2026/7e2h_30957.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 59 5.16 5 C 4800 2.51 5 N 1120 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 7274 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 76} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 6323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6323 Classifications: {'peptide': 824} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 30, 'TRANS': 793} Chain breaks: 3 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'HIS:plan': 3, 'PHE:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 169 Chain: "E" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 336 Unusual residues: {'NAG': 4, 'Y01': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.15, per 1000 atoms: 0.16 Number of scatterers: 7274 At special positions: 0 Unit cell: (102.6, 118.8, 114.48, 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 59 16.00 O 1295 8.00 N 1120 7.00 C 4800 6.00 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 E1609 " - " ASN E 836 " " NAG E1610 " - " ASN E 476 " " NAG E1611 " - " ASN E 363 " " NAG E1612 " - " ASN E 917 " Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 279.5 milliseconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 59.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 188 through 210 removed outlier: 3.987A pdb=" N VAL D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 243 removed outlier: 3.605A pdb=" N VAL D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 5.029A pdb=" N GLN D 261 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 361 through 364 removed outlier: 4.090A pdb=" N ARG E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 364' Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 422 through 430 Processing helix chain 'E' and resid 463 through 472 removed outlier: 4.645A pdb=" N ILE E 467 " --> pdb=" O SER E 463 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 503 removed outlier: 3.755A pdb=" N TYR E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 522 removed outlier: 3.508A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 548 removed outlier: 3.614A pdb=" N THR E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 568 removed outlier: 3.605A pdb=" N ALA E 562 " --> pdb=" O MET E 558 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU E 563 " --> pdb=" O ASN E 559 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE E 564 " --> pdb=" O LEU E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 588 removed outlier: 3.981A pdb=" N ASN E 573 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 574 " --> pdb=" O GLY E 570 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP E 579 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 621 removed outlier: 4.933A pdb=" N LEU E 606 " --> pdb=" O GLN E 602 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N SER E 607 " --> pdb=" O HIS E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 625 Processing helix chain 'E' and resid 628 through 659 removed outlier: 4.334A pdb=" N VAL E 635 " --> pdb=" O ARG E 631 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU E 652 " --> pdb=" O MET E 648 " (cutoff:3.500A) Proline residue: E 653 - end of helix Processing helix chain 'E' and resid 688 through 718 removed outlier: 3.937A pdb=" N LEU E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU E 710 " --> pdb=" O PHE E 706 " (cutoff:3.500A) Proline residue: E 711 - end of helix removed outlier: 4.085A pdb=" N PHE E 717 " --> pdb=" O ILE E 713 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG E 718 " --> pdb=" O VAL E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 738 Processing helix chain 'E' and resid 759 through 767 removed outlier: 3.761A pdb=" N TYR E 764 " --> pdb=" O PRO E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 771 removed outlier: 3.646A pdb=" N LEU E 771 " --> pdb=" O TYR E 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 768 through 771' Processing helix chain 'E' and resid 772 through 780 removed outlier: 4.117A pdb=" N HIS E 778 " --> pdb=" O PHE E 774 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 835 Processing helix chain 'E' and resid 851 through 860 removed outlier: 4.098A pdb=" N THR E 855 " --> pdb=" O CYS E 851 " (cutoff:3.500A) Processing helix chain 'E' and resid 883 through 901 removed outlier: 3.990A pdb=" N LEU E 888 " --> pdb=" O GLU E 884 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS E 891 " --> pdb=" O GLU E 887 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET E 895 " --> pdb=" O LYS E 891 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU E 896 " --> pdb=" O ARG E 892 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG E 899 " --> pdb=" O MET E 895 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER E 900 " --> pdb=" O GLU E 896 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR E 901 " --> pdb=" O LEU E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 952 Processing helix chain 'E' and resid 972 through 1004 removed outlier: 4.282A pdb=" N LEU E 985 " --> pdb=" O SER E 981 " (cutoff:3.500A) Processing helix chain 'E' and resid 1005 through 1031 Processing helix chain 'E' and resid 1037 through 1061 removed outlier: 4.650A pdb=" N SER E1043 " --> pdb=" O SER E1039 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL E1046 " --> pdb=" O ILE E1042 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E1047 " --> pdb=" O SER E1043 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL E1050 " --> pdb=" O VAL E1046 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN E1051 " --> pdb=" O GLY E1047 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E1052 " --> pdb=" O LEU E1048 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E1053 " --> pdb=" O SER E1049 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS E1055 " --> pdb=" O ASN E1051 " (cutoff:3.500A) Processing helix chain 'E' and resid 1071 through 1095 removed outlier: 3.670A pdb=" N SER E1075 " --> pdb=" O LYS E1071 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER E1081 " --> pdb=" O SER E1077 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ALA E1082 " --> pdb=" O ARG E1078 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1129 removed outlier: 4.063A pdb=" N THR E1106 " --> pdb=" O VAL E1102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E1118 " --> pdb=" O LEU E1114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E1121 " --> pdb=" O CYS E1117 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE E1127 " --> pdb=" O ALA E1123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 451 through 459 removed outlier: 4.259A pdb=" N SER E 301 " --> pdb=" O SER E 456 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG E 302 " --> pdb=" O ILE E 487 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE E 487 " --> pdb=" O ARG E 302 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 304 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 787 through 790 Processing sheet with id=AA3, first strand: chain 'E' and resid 913 through 914 removed outlier: 3.789A pdb=" N ALA E 922 " --> pdb=" O ARG E 913 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1068 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: 0.70 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1113 1.32 - 1.44: 2065 1.44 - 1.56: 4208 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 7478 Sorted by residual: bond pdb=" C1 NAG E1609 " pdb=" O5 NAG E1609 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" N VAL E1058 " pdb=" CA VAL E1058 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.48e+00 bond pdb=" N ARG E1061 " pdb=" CA ARG E1061 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.88e+00 bond pdb=" N TYR E1060 " pdb=" CA TYR E1060 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.72e+00 bond pdb=" N LEU E 449 " pdb=" CA LEU E 449 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.38e-02 5.25e+03 5.10e+00 ... (remaining 7473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 9950 1.89 - 3.78: 248 3.78 - 5.67: 30 5.67 - 7.56: 8 7.56 - 9.45: 1 Bond angle restraints: 10237 Sorted by residual: angle pdb=" N VAL E1040 " pdb=" CA VAL E1040 " pdb=" C VAL E1040 " ideal model delta sigma weight residual 111.81 108.91 2.90 8.60e-01 1.35e+00 1.13e+01 angle pdb=" C LYS E 882 " pdb=" N GLN E 883 " pdb=" CA GLN E 883 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C PHE D 255 " pdb=" N LYS D 256 " pdb=" CA LYS D 256 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.26e+00 angle pdb=" N LYS D 256 " pdb=" CA LYS D 256 " pdb=" C LYS D 256 " ideal model delta sigma weight residual 110.80 116.84 -6.04 2.13e+00 2.20e-01 8.04e+00 angle pdb=" CA ARG E1061 " pdb=" C ARG E1061 " pdb=" O ARG E1061 " ideal model delta sigma weight residual 121.81 118.49 3.32 1.18e+00 7.18e-01 7.93e+00 ... (remaining 10232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3832 17.58 - 35.16: 344 35.16 - 52.74: 62 52.74 - 70.32: 13 70.32 - 87.90: 2 Dihedral angle restraints: 4253 sinusoidal: 1589 harmonic: 2664 Sorted by residual: dihedral pdb=" CA PHE E 550 " pdb=" C PHE E 550 " pdb=" N HIS E 551 " pdb=" CA HIS E 551 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS D 256 " pdb=" C LYS D 256 " pdb=" N TYR D 257 " pdb=" CA TYR D 257 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE E 305 " pdb=" C PHE E 305 " pdb=" N THR E 306 " pdb=" CA THR E 306 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 1206 0.189 - 0.378: 1 0.378 - 0.567: 0 0.567 - 0.756: 2 0.756 - 0.945: 2 Chirality restraints: 1211 Sorted by residual: chirality pdb=" C1 NAG E1612 " pdb=" ND2 ASN E 917 " pdb=" C2 NAG E1612 " pdb=" O5 NAG E1612 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" C1 NAG E1610 " pdb=" ND2 ASN E 476 " pdb=" C2 NAG E1610 " pdb=" O5 NAG E1610 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C1 NAG E1609 " pdb=" ND2 ASN E 836 " pdb=" C2 NAG E1609 " pdb=" O5 NAG E1609 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.97e+00 ... (remaining 1208 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 909 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO E 910 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 910 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 910 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 883 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C GLN E 883 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN E 883 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU E 884 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 882 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LYS E 882 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS E 882 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN E 883 " 0.008 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 62 2.62 - 3.19: 6888 3.19 - 3.76: 10409 3.76 - 4.33: 13591 4.33 - 4.90: 22719 Nonbonded interactions: 53669 Sorted by model distance: nonbonded pdb=" OH TYR D 253 " pdb=" OD1 ASP E 813 " model vdw 2.045 3.040 nonbonded pdb=" O SER E 820 " pdb=" OG SER E 823 " model vdw 2.199 3.040 nonbonded pdb=" OG SER E 308 " pdb=" O GLY E 480 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR E 543 " pdb=" NH1 ARG E 547 " model vdw 2.267 3.120 nonbonded pdb=" N GLU E1038 " pdb=" OE1 GLU E1038 " model vdw 2.286 3.120 ... (remaining 53664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.390 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.004 0.089 7482 Z= 0.212 Angle : 0.736 11.157 10249 Z= 0.382 Chirality : 0.061 0.945 1211 Planarity : 0.004 0.049 1228 Dihedral : 13.909 87.902 2525 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.47 % Favored : 91.30 % Rotamer: Outliers : 0.55 % Allowed : 7.97 % Favored : 91.48 % 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: -3.54 (0.25), residues: 897 helix: -1.39 (0.21), residues: 481 sheet: -1.76 (0.92), residues: 31 loop : -3.71 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1132 TYR 0.015 0.001 TYR E 620 PHE 0.019 0.001 PHE E 552 TRP 0.020 0.001 TRP E 651 HIS 0.003 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 ( 7478) covalent geometry : angle 0.70850 / 0.38 (10237) hydrogen bonds : bond 0.14944 / 10.04 ( 363) hydrogen bonds : angle 6.15126 / 4.27 ( 1068) link_NAG-ASN : bond 0.02149 / 1.08 ( 4) link_NAG-ASN : angle 5.89809 / 3.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 623 TYR cc_start: 0.8700 (t80) cc_final: 0.8476 (t80) REVERT: E 805 LYS cc_start: 0.8970 (tptt) cc_final: 0.8608 (tptp) REVERT: E 940 MET cc_start: 0.9012 (mmm) cc_final: 0.8782 (mmm) REVERT: E 986 ILE cc_start: 0.8761 (mm) cc_final: 0.8525 (mt) REVERT: E 1042 ILE cc_start: 0.9216 (mm) cc_final: 0.8851 (mt) REVERT: E 1051 ASN cc_start: 0.8541 (t0) cc_final: 0.8197 (t0) REVERT: E 1061 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7214 (ttp-170) outliers start: 4 outliers final: 0 residues processed: 143 average time/residue: 0.0618 time to fit residues: 12.3316 Evaluate side-chains 112 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1061 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 ASN E 315 ASN E 497 GLN E 622 ASN ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 GLN E 977 GLN E1035 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104087 restraints weight = 12955.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107611 restraints weight = 6878.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109999 restraints weight = 4674.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111654 restraints weight = 3661.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112344 restraints weight = 3106.029| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7482 Z= 0.126 Angle : 0.689 12.964 10249 Z= 0.332 Chirality : 0.042 0.287 1211 Planarity : 0.004 0.050 1228 Dihedral : 7.725 59.945 1068 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 1.65 % Allowed : 16.48 % Favored : 81.87 % 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: -1.81 (0.28), residues: 897 helix: 0.19 (0.23), residues: 487 sheet: 0.12 (1.05), residues: 25 loop : -3.28 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1132 TYR 0.012 0.001 TYR E 620 PHE 0.017 0.001 PHE E 436 TRP 0.018 0.001 TRP E 651 HIS 0.004 0.001 HIS E 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 7478) covalent geometry : angle 0.68554 / 0.33 (10237) hydrogen bonds : bond 0.04759 / 3.12 ( 363) hydrogen bonds : angle 4.32216 / 2.98 ( 1068) link_NAG-ASN : bond 0.00698 / 0.35 ( 4) link_NAG-ASN : angle 2.22693 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 805 LYS cc_start: 0.8941 (tptt) cc_final: 0.8318 (tptt) REVERT: E 1003 THR cc_start: 0.7908 (m) cc_final: 0.7438 (m) REVERT: E 1051 ASN cc_start: 0.8402 (t0) cc_final: 0.8033 (t0) outliers start: 12 outliers final: 9 residues processed: 150 average time/residue: 0.0584 time to fit residues: 12.8003 Evaluate side-chains 130 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 968 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1096 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 800 ASN E1055 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098575 restraints weight = 12986.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101624 restraints weight = 7321.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103124 restraints weight = 5201.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104607 restraints weight = 4118.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104652 restraints weight = 3806.388| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7482 Z= 0.234 Angle : 0.763 11.987 10249 Z= 0.372 Chirality : 0.045 0.284 1211 Planarity : 0.004 0.052 1228 Dihedral : 7.666 58.416 1064 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 3.30 % Allowed : 22.25 % Favored : 74.45 % 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: -1.47 (0.28), residues: 897 helix: 0.55 (0.24), residues: 486 sheet: 0.18 (1.09), residues: 25 loop : -3.22 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1068 TYR 0.027 0.002 TYR E1011 PHE 0.027 0.002 PHE E 586 TRP 0.031 0.002 TRP E 352 HIS 0.005 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 ( 7478) covalent geometry : angle 0.75984 / 0.37 (10237) hydrogen bonds : bond 0.06102 / 4.02 ( 363) hydrogen bonds : angle 4.37253 / 3.00 ( 1068) link_NAG-ASN : bond 0.00387 / 0.19 ( 4) link_NAG-ASN : angle 2.02387 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: E 805 LYS cc_start: 0.9005 (tptt) cc_final: 0.8575 (tptp) REVERT: E 1051 ASN cc_start: 0.8619 (t0) cc_final: 0.8291 (t0) REVERT: E 1097 MET cc_start: 0.8980 (mmp) cc_final: 0.8510 (mmp) REVERT: E 1130 MET cc_start: 0.8487 (tpp) cc_final: 0.8240 (tpp) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 0.0484 time to fit residues: 9.9297 Evaluate side-chains 126 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 584 THR Chi-restraints excluded: chain E residue 627 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 968 VAL Chi-restraints excluded: chain E residue 992 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1096 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 800 ASN E 964 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104900 restraints weight = 12643.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108465 restraints weight = 6656.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110822 restraints weight = 4473.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112507 restraints weight = 3498.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113339 restraints weight = 2971.004| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7482 Z= 0.121 Angle : 0.683 13.117 10249 Z= 0.325 Chirality : 0.042 0.228 1211 Planarity : 0.004 0.054 1228 Dihedral : 7.149 58.138 1064 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 2.88 % Allowed : 22.53 % Favored : 74.59 % 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: -1.08 (0.29), residues: 897 helix: 0.89 (0.24), residues: 487 sheet: 0.85 (1.10), residues: 25 loop : -3.13 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1068 TYR 0.034 0.001 TYR E1011 PHE 0.014 0.001 PHE E 436 TRP 0.023 0.002 TRP E 352 HIS 0.002 0.000 HIS E 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7478) covalent geometry : angle 0.68084 / 0.32 (10237) hydrogen bonds : bond 0.04517 / 2.92 ( 363) hydrogen bonds : angle 4.05795 / 2.79 ( 1068) link_NAG-ASN : bond 0.00535 / 0.26 ( 4) link_NAG-ASN : angle 1.70760 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: E 805 LYS cc_start: 0.8919 (tptt) cc_final: 0.8539 (tptp) REVERT: E 1003 THR cc_start: 0.7830 (m) cc_final: 0.7541 (m) REVERT: E 1051 ASN cc_start: 0.8346 (t0) cc_final: 0.8004 (t0) REVERT: E 1097 MET cc_start: 0.8931 (mmp) cc_final: 0.8500 (mmp) outliers start: 21 outliers final: 11 residues processed: 143 average time/residue: 0.0466 time to fit residues: 10.1120 Evaluate side-chains 127 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 558 MET Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1096 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 798 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105930 restraints weight = 12684.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109473 restraints weight = 6763.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111928 restraints weight = 4605.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113553 restraints weight = 3617.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114612 restraints weight = 3097.999| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7482 Z= 0.114 Angle : 0.665 13.129 10249 Z= 0.315 Chirality : 0.041 0.223 1211 Planarity : 0.004 0.052 1228 Dihedral : 6.847 59.200 1064 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.61 % Allowed : 24.18 % Favored : 73.21 % 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: -0.89 (0.29), residues: 897 helix: 1.01 (0.24), residues: 487 sheet: 1.38 (1.12), residues: 25 loop : -3.03 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1068 TYR 0.033 0.001 TYR E1011 PHE 0.024 0.001 PHE E 586 TRP 0.018 0.001 TRP E 651 HIS 0.001 0.000 HIS E 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7478) covalent geometry : angle 0.66338 / 0.31 (10237) hydrogen bonds : bond 0.04167 / 2.69 ( 363) hydrogen bonds : angle 3.96879 / 2.73 ( 1068) link_NAG-ASN : bond 0.00496 / 0.25 ( 4) link_NAG-ASN : angle 1.61358 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8788 (tt) cc_final: 0.8562 (tt) REVERT: E 805 LYS cc_start: 0.8929 (tptt) cc_final: 0.8517 (tptp) REVERT: E 955 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6495 (pp) REVERT: E 996 PHE cc_start: 0.8180 (t80) cc_final: 0.7979 (t80) REVERT: E 1003 THR cc_start: 0.7803 (m) cc_final: 0.7488 (m) REVERT: E 1051 ASN cc_start: 0.8393 (t0) cc_final: 0.8038 (t0) REVERT: E 1097 MET cc_start: 0.8916 (mmp) cc_final: 0.8424 (mmp) REVERT: E 1112 MET cc_start: 0.8134 (tpp) cc_final: 0.7499 (mtt) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.0437 time to fit residues: 9.3366 Evaluate side-chains 126 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1096 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 0.0050 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 474 ASN E 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109901 restraints weight = 13228.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113639 restraints weight = 6688.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116162 restraints weight = 4472.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117355 restraints weight = 3513.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118709 restraints weight = 3075.478| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7482 Z= 0.123 Angle : 0.669 12.886 10249 Z= 0.317 Chirality : 0.041 0.220 1211 Planarity : 0.004 0.051 1228 Dihedral : 6.791 59.697 1064 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.02 % Allowed : 24.45 % Favored : 72.53 % 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: -0.76 (0.29), residues: 897 helix: 1.10 (0.24), residues: 487 sheet: 1.66 (1.12), residues: 25 loop : -2.95 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E1068 TYR 0.044 0.001 TYR E1011 PHE 0.014 0.001 PHE E 552 TRP 0.021 0.001 TRP E 859 HIS 0.001 0.000 HIS E 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7478) covalent geometry : angle 0.66701 / 0.32 (10237) hydrogen bonds : bond 0.04373 / 2.84 ( 363) hydrogen bonds : angle 3.93570 / 2.71 ( 1068) link_NAG-ASN : bond 0.00435 / 0.21 ( 4) link_NAG-ASN : angle 1.55873 / 0.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8800 (tt) cc_final: 0.8580 (tt) REVERT: E 658 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8620 (tt) REVERT: E 805 LYS cc_start: 0.8887 (tptt) cc_final: 0.8514 (tptp) REVERT: E 895 MET cc_start: 0.8562 (mmm) cc_final: 0.8345 (tpt) REVERT: E 955 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6391 (pp) REVERT: E 1003 THR cc_start: 0.7824 (m) cc_final: 0.7530 (m) REVERT: E 1051 ASN cc_start: 0.8309 (t0) cc_final: 0.7964 (t0) REVERT: E 1097 MET cc_start: 0.8839 (mmp) cc_final: 0.8476 (mmp) REVERT: E 1112 MET cc_start: 0.8017 (tpp) cc_final: 0.7496 (mtt) outliers start: 22 outliers final: 13 residues processed: 137 average time/residue: 0.0441 time to fit residues: 9.5625 Evaluate side-chains 132 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 992 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1096 MET Chi-restraints excluded: chain E residue 1114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 603 HIS E 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.141250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110956 restraints weight = 13126.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114774 restraints weight = 6584.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117355 restraints weight = 4367.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118901 restraints weight = 3409.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120028 restraints weight = 2931.203| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7482 Z= 0.118 Angle : 0.693 15.981 10249 Z= 0.319 Chirality : 0.041 0.223 1211 Planarity : 0.004 0.051 1228 Dihedral : 6.758 59.921 1064 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 3.57 % Allowed : 24.45 % Favored : 71.98 % 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: -0.68 (0.29), residues: 897 helix: 1.16 (0.24), residues: 487 sheet: 1.85 (1.12), residues: 25 loop : -2.93 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 331 TYR 0.023 0.001 TYR E1011 PHE 0.023 0.001 PHE E 996 TRP 0.040 0.002 TRP E 352 HIS 0.008 0.001 HIS E 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7478) covalent geometry : angle 0.69109 / 0.32 (10237) hydrogen bonds : bond 0.04138 / 2.68 ( 363) hydrogen bonds : angle 3.88271 / 2.69 ( 1068) link_NAG-ASN : bond 0.00447 / 0.22 ( 4) link_NAG-ASN : angle 1.49687 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8814 (tt) cc_final: 0.8584 (tt) REVERT: E 805 LYS cc_start: 0.8904 (tptt) cc_final: 0.8512 (tptp) REVERT: E 955 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6428 (pp) REVERT: E 1003 THR cc_start: 0.7744 (m) cc_final: 0.7447 (m) REVERT: E 1051 ASN cc_start: 0.8358 (t0) cc_final: 0.8018 (t0) REVERT: E 1097 MET cc_start: 0.8916 (mmp) cc_final: 0.8520 (mmp) REVERT: E 1112 MET cc_start: 0.7970 (tpp) cc_final: 0.7421 (mtt) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.0468 time to fit residues: 10.4348 Evaluate side-chains 135 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 816 PHE Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 992 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1092 VAL Chi-restraints excluded: chain E residue 1096 MET Chi-restraints excluded: chain E residue 1114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.0020 chunk 23 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 603 HIS E 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111680 restraints weight = 13099.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115480 restraints weight = 6603.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118042 restraints weight = 4387.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119507 restraints weight = 3430.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120675 restraints weight = 2970.196| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7482 Z= 0.117 Angle : 0.689 12.880 10249 Z= 0.320 Chirality : 0.041 0.224 1211 Planarity : 0.004 0.050 1228 Dihedral : 6.678 59.813 1064 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.88 % Allowed : 25.96 % Favored : 71.15 % 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: -0.60 (0.29), residues: 897 helix: 1.20 (0.24), residues: 487 sheet: 1.98 (1.11), residues: 25 loop : -2.85 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 331 TYR 0.014 0.001 TYR E1011 PHE 0.012 0.001 PHE E 552 TRP 0.018 0.001 TRP E 651 HIS 0.012 0.001 HIS E 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7478) covalent geometry : angle 0.68757 / 0.32 (10237) hydrogen bonds : bond 0.04076 / 2.64 ( 363) hydrogen bonds : angle 3.88216 / 2.70 ( 1068) link_NAG-ASN : bond 0.00450 / 0.22 ( 4) link_NAG-ASN : angle 1.46209 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8800 (tt) cc_final: 0.8569 (tt) REVERT: E 658 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8606 (tt) REVERT: E 805 LYS cc_start: 0.8863 (tptt) cc_final: 0.8487 (tptp) REVERT: E 895 MET cc_start: 0.8491 (mmm) cc_final: 0.8290 (tpt) REVERT: E 1003 THR cc_start: 0.7812 (m) cc_final: 0.7527 (m) REVERT: E 1051 ASN cc_start: 0.8346 (t0) cc_final: 0.8015 (t0) REVERT: E 1097 MET cc_start: 0.8902 (mmp) cc_final: 0.8513 (mmp) REVERT: E 1112 MET cc_start: 0.7952 (tpp) cc_final: 0.7492 (mtt) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.0536 time to fit residues: 10.8182 Evaluate side-chains 135 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 816 PHE Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 992 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1096 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108113 restraints weight = 13005.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111795 restraints weight = 6679.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114266 restraints weight = 4496.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115434 restraints weight = 3541.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116694 restraints weight = 3117.403| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7482 Z= 0.157 Angle : 0.703 12.477 10249 Z= 0.333 Chirality : 0.042 0.217 1211 Planarity : 0.004 0.050 1228 Dihedral : 6.787 59.325 1064 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.30 % Allowed : 25.69 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.62 (0.29), residues: 897 helix: 1.18 (0.24), residues: 487 sheet: 1.80 (1.12), residues: 25 loop : -2.84 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 329 TYR 0.015 0.001 TYR E 546 PHE 0.026 0.001 PHE E 996 TRP 0.019 0.001 TRP E 651 HIS 0.015 0.001 HIS E 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 7478) covalent geometry : angle 0.70167 / 0.33 (10237) hydrogen bonds : bond 0.04615 / 3.00 ( 363) hydrogen bonds : angle 3.91347 / 2.72 ( 1068) link_NAG-ASN : bond 0.00310 / 0.15 ( 4) link_NAG-ASN : angle 1.47021 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8826 (tt) cc_final: 0.8585 (tt) REVERT: E 658 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 805 LYS cc_start: 0.8937 (tptt) cc_final: 0.8538 (tptp) REVERT: E 895 MET cc_start: 0.8598 (mmm) cc_final: 0.8380 (tpt) REVERT: E 1003 THR cc_start: 0.8061 (m) cc_final: 0.7811 (m) REVERT: E 1051 ASN cc_start: 0.8400 (t0) cc_final: 0.8039 (t0) REVERT: E 1097 MET cc_start: 0.8892 (mmp) cc_final: 0.8476 (mmp) REVERT: E 1112 MET cc_start: 0.8060 (tpp) cc_final: 0.7482 (mtt) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.0477 time to fit residues: 9.9803 Evaluate side-chains 133 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 816 PHE Chi-restraints excluded: chain E residue 853 ILE Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 992 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1096 MET Chi-restraints excluded: chain E residue 1130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.0000 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110165 restraints weight = 13088.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113949 restraints weight = 6660.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116480 restraints weight = 4428.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118098 restraints weight = 3469.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118946 restraints weight = 2978.577| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7482 Z= 0.123 Angle : 0.690 12.799 10249 Z= 0.324 Chirality : 0.041 0.219 1211 Planarity : 0.004 0.051 1228 Dihedral : 6.743 59.369 1064 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.47 % Allowed : 26.51 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.58 (0.29), residues: 897 helix: 1.20 (0.24), residues: 487 sheet: 1.87 (1.11), residues: 25 loop : -2.82 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 331 TYR 0.013 0.001 TYR E1011 PHE 0.014 0.001 PHE E 552 TRP 0.018 0.001 TRP E 651 HIS 0.011 0.001 HIS E 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7478) covalent geometry : angle 0.68890 / 0.32 (10237) hydrogen bonds : bond 0.04350 / 2.81 ( 363) hydrogen bonds : angle 3.85854 / 2.68 ( 1068) link_NAG-ASN : bond 0.00417 / 0.21 ( 4) link_NAG-ASN : angle 1.44132 / 0.73 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8787 (tt) cc_final: 0.8547 (tt) REVERT: E 658 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8641 (tt) REVERT: E 805 LYS cc_start: 0.8902 (tptt) cc_final: 0.8515 (tptp) REVERT: E 895 MET cc_start: 0.8583 (mmm) cc_final: 0.8370 (tpt) REVERT: E 1003 THR cc_start: 0.7927 (m) cc_final: 0.7651 (m) REVERT: E 1051 ASN cc_start: 0.8362 (t0) cc_final: 0.8021 (t0) REVERT: E 1097 MET cc_start: 0.8849 (mmp) cc_final: 0.8511 (mmp) REVERT: E 1112 MET cc_start: 0.7976 (tpp) cc_final: 0.7384 (mtt) outliers start: 18 outliers final: 17 residues processed: 132 average time/residue: 0.0532 time to fit residues: 10.8365 Evaluate side-chains 136 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 816 PHE Chi-restraints excluded: chain E residue 853 ILE Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 992 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1049 SER Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1096 MET Chi-restraints excluded: chain E residue 1130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 9.9990 chunk 14 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.5672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111911 restraints weight = 13091.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115719 restraints weight = 6624.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118298 restraints weight = 4415.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119963 restraints weight = 3450.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120877 restraints weight = 2953.471| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7482 Z= 0.115 Angle : 0.679 12.938 10249 Z= 0.319 Chirality : 0.041 0.223 1211 Planarity : 0.004 0.054 1228 Dihedral : 6.635 59.276 1064 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.88 % Allowed : 26.10 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.49 (0.29), residues: 897 helix: 1.26 (0.24), residues: 487 sheet: 2.16 (1.11), residues: 25 loop : -2.77 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 331 TYR 0.014 0.001 TYR E1011 PHE 0.023 0.001 PHE E 586 TRP 0.017 0.001 TRP E 651 HIS 0.009 0.001 HIS E 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7478) covalent geometry : angle 0.67817 / 0.32 (10237) hydrogen bonds : bond 0.04032 / 2.59 ( 363) hydrogen bonds : angle 3.82415 / 2.66 ( 1068) link_NAG-ASN : bond 0.00447 / 0.22 ( 4) link_NAG-ASN : angle 1.39329 / 0.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1113.78 seconds wall clock time: 19 minutes 56.48 seconds (1196.48 seconds total)