Starting phenix.real_space_refine on Wed Mar 12 07:03:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e2h_30957/03_2025/7e2h_30957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2h_30957/03_2025/7e2h_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e2h_30957/03_2025/7e2h_30957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2h_30957/03_2025/7e2h_30957.map" model { file = "/net/cci-nas-00/data/ceres_data/7e2h_30957/03_2025/7e2h_30957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2h_30957/03_2025/7e2h_30957.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ASN:plan1': 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: {'GLN:plan1': 6, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.77, per 1000 atoms: 0.66 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: 2.17 Conformation dependent library (CDL) restraints added in 903.6 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: 0.54 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: 1.66 Time building geometry restraints manager: 2.54 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 - 23.62: 4516 23.62 - 47.24: 256 47.24 - 70.85: 24 70.85 - 94.47: 2 94.47 - 118.09: 3 Dihedral angle restraints: 4801 sinusoidal: 2137 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=" C2 NAG E1609 " pdb=" C1 NAG E1609 " pdb=" O5 NAG E1609 " pdb=" C5 NAG E1609 " ideal model delta sinusoidal sigma weight residual -62.96 55.13 -118.09 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 4798 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: 0.400 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 7478 Z= 0.275 Angle : 0.709 9.447 10237 Z= 0.377 Chirality : 0.061 0.945 1211 Planarity : 0.004 0.049 1228 Dihedral : 13.864 118.087 3073 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.001 TRP E 651 HIS 0.003 0.001 HIS E 493 PHE 0.019 0.001 PHE E 552 TYR 0.015 0.001 TYR E 620 ARG 0.002 0.000 ARG E1132 *********************** 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 : 0.817 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: 0.1906 time to fit residues: 37.4300 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 : 0.837 ------------------------------------------------------------------------------- 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 75 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.0050 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN E 315 ASN E 497 GLN E 622 ASN 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 = 0.3716 r_free = 0.3716 target = 0.133876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104511 restraints weight = 12790.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107896 restraints weight = 6887.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110087 restraints weight = 4715.438| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7478 Z= 0.186 Angle : 0.705 13.654 10237 Z= 0.337 Chirality : 0.043 0.299 1211 Planarity : 0.004 0.050 1228 Dihedral : 9.461 85.842 1616 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 1.79 % Allowed : 16.62 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.28), residues: 897 helix: 0.18 (0.23), residues: 487 sheet: 0.07 (1.05), residues: 25 loop : -3.28 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 651 HIS 0.004 0.000 HIS E 659 PHE 0.017 0.001 PHE E 436 TYR 0.012 0.001 TYR E 620 ARG 0.003 0.000 ARG E1132 *********************** 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 155 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 805 LYS cc_start: 0.8943 (tptt) cc_final: 0.8328 (tptt) REVERT: E 1003 THR cc_start: 0.7940 (m) cc_final: 0.7447 (m) REVERT: E 1051 ASN cc_start: 0.8395 (t0) cc_final: 0.8037 (t0) outliers start: 13 outliers final: 10 residues processed: 150 average time/residue: 0.1541 time to fit residues: 33.3116 Evaluate side-chains 131 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 982 ASP 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 58 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 964 ASN E1055 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103100 restraints weight = 12803.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106577 restraints weight = 6935.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108942 restraints weight = 4773.101| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7478 Z= 0.217 Angle : 0.689 12.619 10237 Z= 0.330 Chirality : 0.042 0.275 1211 Planarity : 0.004 0.050 1228 Dihedral : 9.142 81.415 1612 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 2.88 % Allowed : 20.74 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.29), residues: 897 helix: 0.72 (0.24), residues: 487 sheet: 0.45 (1.05), residues: 25 loop : -3.17 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 352 HIS 0.002 0.000 HIS E 659 PHE 0.021 0.001 PHE E 586 TYR 0.023 0.001 TYR E1011 ARG 0.005 0.000 ARG E1068 *********************** 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 145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 805 LYS cc_start: 0.8975 (tptt) cc_final: 0.8567 (tptp) REVERT: E 1003 THR cc_start: 0.7930 (m) cc_final: 0.7626 (m) REVERT: E 1051 ASN cc_start: 0.8351 (t0) cc_final: 0.7932 (t0) REVERT: E 1130 MET cc_start: 0.8390 (tpp) cc_final: 0.8138 (tpp) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 0.1404 time to fit residues: 28.5588 Evaluate side-chains 127 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102250 restraints weight = 12639.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105664 restraints weight = 6943.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107991 restraints weight = 4802.514| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7478 Z= 0.227 Angle : 0.706 12.516 10237 Z= 0.334 Chirality : 0.043 0.257 1211 Planarity : 0.004 0.053 1228 Dihedral : 8.937 72.800 1612 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 2.88 % Allowed : 22.25 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.29), residues: 897 helix: 0.84 (0.24), residues: 487 sheet: 0.72 (1.07), residues: 25 loop : -3.11 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 352 HIS 0.002 0.000 HIS E 493 PHE 0.017 0.001 PHE E 552 TYR 0.036 0.001 TYR E1011 ARG 0.003 0.000 ARG E1068 *********************** 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 145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 805 LYS cc_start: 0.8976 (tptt) cc_final: 0.8567 (tptp) REVERT: E 1003 THR cc_start: 0.7949 (m) cc_final: 0.7639 (m) REVERT: E 1051 ASN cc_start: 0.8427 (t0) cc_final: 0.8027 (t0) outliers start: 21 outliers final: 15 residues processed: 137 average time/residue: 0.1740 time to fit residues: 36.1755 Evaluate side-chains 129 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 584 THR 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 1076 LEU Chi-restraints excluded: chain E residue 1092 VAL 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 78 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104240 restraints weight = 12680.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107759 restraints weight = 6859.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110172 restraints weight = 4698.642| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7478 Z= 0.188 Angle : 0.679 13.047 10237 Z= 0.321 Chirality : 0.041 0.234 1211 Planarity : 0.004 0.053 1228 Dihedral : 8.607 58.978 1612 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.61 % Allowed : 23.49 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.29), residues: 897 helix: 0.96 (0.24), residues: 487 sheet: 1.11 (1.09), residues: 25 loop : -3.03 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 651 HIS 0.001 0.000 HIS E 941 PHE 0.023 0.001 PHE E 586 TYR 0.048 0.001 TYR E1011 ARG 0.002 0.000 ARG E1068 *********************** 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 146 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 805 LYS cc_start: 0.8958 (tptt) cc_final: 0.8553 (tptp) REVERT: E 955 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6453 (pp) REVERT: E 1003 THR cc_start: 0.7928 (m) cc_final: 0.7627 (m) REVERT: E 1051 ASN cc_start: 0.8365 (t0) cc_final: 0.7979 (t0) outliers start: 19 outliers final: 12 residues processed: 140 average time/residue: 0.1414 time to fit residues: 29.2897 Evaluate side-chains 129 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 515 LEU Chi-restraints excluded: chain E residue 567 VAL 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 955 LEU 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 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 8 optimal weight: 0.0970 chunk 12 optimal weight: 8.9990 chunk 38 optimal weight: 0.0000 chunk 48 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114256 restraints weight = 12920.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118102 restraints weight = 6467.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120735 restraints weight = 4246.351| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7478 Z= 0.163 Angle : 0.673 13.296 10237 Z= 0.315 Chirality : 0.040 0.209 1211 Planarity : 0.004 0.052 1228 Dihedral : 8.035 58.796 1612 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.20 % Allowed : 25.55 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.29), residues: 897 helix: 1.09 (0.24), residues: 487 sheet: 1.67 (1.15), residues: 25 loop : -2.98 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 651 HIS 0.001 0.000 HIS E 659 PHE 0.012 0.001 PHE E 436 TYR 0.015 0.001 TYR E1011 ARG 0.002 0.000 ARG E1132 *********************** 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 156 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8761 (tt) cc_final: 0.8540 (tt) REVERT: E 805 LYS cc_start: 0.8863 (tptt) cc_final: 0.8503 (tptp) REVERT: E 895 MET cc_start: 0.8562 (mmm) cc_final: 0.8360 (tpt) REVERT: E 1003 THR cc_start: 0.7615 (m) cc_final: 0.7298 (m) REVERT: E 1051 ASN cc_start: 0.8218 (t0) cc_final: 0.7935 (t0) REVERT: E 1112 MET cc_start: 0.7915 (tpp) cc_final: 0.7404 (mtt) outliers start: 16 outliers final: 8 residues processed: 150 average time/residue: 0.1356 time to fit residues: 30.0698 Evaluate side-chains 127 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 567 VAL Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 1020 ILE Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1092 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 603 HIS ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112915 restraints weight = 12980.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116698 restraints weight = 6517.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119331 restraints weight = 4359.456| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7478 Z= 0.167 Angle : 0.695 16.990 10237 Z= 0.321 Chirality : 0.041 0.236 1211 Planarity : 0.004 0.051 1228 Dihedral : 7.925 59.179 1612 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.58 % Favored : 93.31 % Rotamer: Outliers : 2.88 % Allowed : 24.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.28), residues: 897 helix: 1.14 (0.24), residues: 487 sheet: 1.80 (1.12), residues: 25 loop : -2.92 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 352 HIS 0.008 0.001 HIS E 603 PHE 0.023 0.001 PHE E 996 TYR 0.011 0.001 TYR E 546 ARG 0.001 0.000 ARG E 331 *********************** 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 146 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8776 (tt) cc_final: 0.8561 (tt) REVERT: E 805 LYS cc_start: 0.8905 (tptt) cc_final: 0.8535 (tptp) REVERT: E 1003 THR cc_start: 0.7777 (m) cc_final: 0.7496 (m) REVERT: E 1051 ASN cc_start: 0.8220 (t0) cc_final: 0.7905 (t0) REVERT: E 1112 MET cc_start: 0.7883 (tpp) cc_final: 0.7478 (mtt) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.1513 time to fit residues: 30.2956 Evaluate side-chains 136 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 572 ASN Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 924 VAL Chi-restraints excluded: chain E residue 1020 ILE 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 Chi-restraints excluded: chain E residue 1122 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 603 HIS ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112026 restraints weight = 13113.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115779 restraints weight = 6598.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118418 restraints weight = 4393.336| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7478 Z= 0.183 Angle : 0.684 12.691 10237 Z= 0.321 Chirality : 0.041 0.219 1211 Planarity : 0.004 0.054 1228 Dihedral : 7.970 59.142 1612 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 2.34 % Allowed : 25.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 897 helix: 1.18 (0.24), residues: 487 sheet: 1.82 (1.12), residues: 25 loop : -2.86 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 859 HIS 0.009 0.001 HIS E 603 PHE 0.015 0.001 PHE E 552 TYR 0.012 0.001 TYR E 546 ARG 0.001 0.000 ARG E 331 *********************** 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 148 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8766 (tt) cc_final: 0.8550 (tt) REVERT: E 658 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8564 (tt) REVERT: E 805 LYS cc_start: 0.8900 (tptt) cc_final: 0.8526 (tptp) REVERT: E 895 MET cc_start: 0.8597 (mmm) cc_final: 0.8397 (tpt) REVERT: E 1003 THR cc_start: 0.7850 (m) cc_final: 0.7579 (m) REVERT: E 1051 ASN cc_start: 0.8346 (t0) cc_final: 0.8034 (t0) REVERT: E 1112 MET cc_start: 0.7934 (tpp) cc_final: 0.7450 (mtt) outliers start: 17 outliers final: 14 residues processed: 141 average time/residue: 0.1367 time to fit residues: 28.9655 Evaluate side-chains 139 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 924 VAL Chi-restraints excluded: chain E residue 1020 ILE 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 Chi-restraints excluded: chain E residue 1122 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 603 HIS ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112471 restraints weight = 13130.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116341 restraints weight = 6600.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118922 restraints weight = 4394.627| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7478 Z= 0.173 Angle : 0.689 12.810 10237 Z= 0.321 Chirality : 0.041 0.215 1211 Planarity : 0.004 0.053 1228 Dihedral : 7.930 57.681 1612 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.34 % Allowed : 25.96 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 897 helix: 1.23 (0.24), residues: 487 sheet: 1.90 (1.13), residues: 25 loop : -2.82 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 859 HIS 0.010 0.001 HIS E 603 PHE 0.020 0.001 PHE E 586 TYR 0.012 0.001 TYR E 546 ARG 0.001 0.000 ARG E 331 *********************** 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 142 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8758 (tt) cc_final: 0.8546 (tt) REVERT: E 658 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8593 (tt) REVERT: E 805 LYS cc_start: 0.8900 (tptt) cc_final: 0.8522 (tptp) REVERT: E 895 MET cc_start: 0.8618 (mmm) cc_final: 0.8405 (tpt) REVERT: E 1003 THR cc_start: 0.7836 (m) cc_final: 0.7570 (m) REVERT: E 1051 ASN cc_start: 0.8319 (t0) cc_final: 0.8017 (t0) REVERT: E 1112 MET cc_start: 0.7894 (tpp) cc_final: 0.7461 (mtt) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.1376 time to fit residues: 27.5652 Evaluate side-chains 138 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 924 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 Chi-restraints excluded: chain E residue 1114 LEU Chi-restraints excluded: chain E residue 1122 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.0020 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108719 restraints weight = 13308.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112422 restraints weight = 6753.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114928 restraints weight = 4515.809| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7478 Z= 0.239 Angle : 0.704 12.500 10237 Z= 0.335 Chirality : 0.042 0.225 1211 Planarity : 0.004 0.053 1228 Dihedral : 8.022 57.050 1612 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.06 % Allowed : 26.37 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 897 helix: 1.20 (0.24), residues: 487 sheet: 1.74 (1.13), residues: 25 loop : -2.80 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 651 HIS 0.010 0.001 HIS E 603 PHE 0.020 0.001 PHE E 552 TYR 0.014 0.001 TYR E 546 ARG 0.002 0.000 ARG E 329 ********************** 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 136 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 566 LEU cc_start: 0.8791 (tt) cc_final: 0.8569 (tt) REVERT: E 658 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8656 (tt) REVERT: E 805 LYS cc_start: 0.8977 (tptt) cc_final: 0.8565 (tptp) REVERT: E 895 MET cc_start: 0.8656 (mmm) cc_final: 0.8447 (tpt) REVERT: E 1003 THR cc_start: 0.7992 (m) cc_final: 0.7729 (m) REVERT: E 1051 ASN cc_start: 0.8396 (t0) cc_final: 0.8038 (t0) REVERT: E 1112 MET cc_start: 0.8022 (tpp) cc_final: 0.7510 (mtt) outliers start: 15 outliers final: 14 residues processed: 130 average time/residue: 0.1439 time to fit residues: 27.8532 Evaluate side-chains 134 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 747 LEU Chi-restraints excluded: chain E residue 924 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 Chi-restraints excluded: chain E residue 1114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.0050 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 603 HIS ** E 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111866 restraints weight = 13031.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115711 restraints weight = 6583.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118283 restraints weight = 4390.833| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7478 Z= 0.169 Angle : 0.681 12.919 10237 Z= 0.321 Chirality : 0.041 0.211 1211 Planarity : 0.004 0.053 1228 Dihedral : 7.910 56.955 1612 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.20 % Allowed : 26.37 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 897 helix: 1.28 (0.24), residues: 487 sheet: 1.89 (1.14), residues: 25 loop : -2.74 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 651 HIS 0.009 0.001 HIS E 603 PHE 0.023 0.001 PHE E 586 TYR 0.011 0.001 TYR E 546 ARG 0.002 0.000 ARG E 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2384.87 seconds wall clock time: 42 minutes 12.95 seconds (2532.95 seconds total)