Starting phenix.real_space_refine on Fri Mar 14 00:02:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8r_44356/03_2025/9b8r_44356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8r_44356/03_2025/9b8r_44356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8r_44356/03_2025/9b8r_44356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8r_44356/03_2025/9b8r_44356.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8r_44356/03_2025/9b8r_44356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8r_44356/03_2025/9b8r_44356.cif" } resolution = 3.5 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= 0.002 sd= 0.047 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 22 5.49 5 S 47 5.16 5 C 5939 2.51 5 N 1590 2.21 5 O 1823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9425 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 8967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8967 Classifications: {'peptide': 1119} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1066} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5209 SG CYS E 665 45.858 64.745 17.877 1.00 81.51 S ATOM 5297 SG CYS E 677 52.149 64.661 17.029 1.00 87.54 S ATOM 6033 SG CYS E 763 51.160 66.480 22.121 1.00 94.87 S ATOM 5226 SG CYS E 668 49.284 70.341 17.828 1.00 78.76 S Time building chain proxies: 5.72, per 1000 atoms: 0.61 Number of scatterers: 9425 At special positions: 0 Unit cell: (100.188, 110.952, 106.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 47 16.00 P 22 15.00 O 1823 8.00 N 1590 7.00 C 5939 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 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 978.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 E1401 " pdb="FE4 SF4 E1401 " - pdb=" SG CYS E 668 " pdb="FE1 SF4 E1401 " - pdb=" SG CYS E 665 " pdb="FE2 SF4 E1401 " - pdb=" SG CYS E 677 " pdb="FE3 SF4 E1401 " - pdb=" SG CYS E 763 " Number of angles added : 12 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 49.2% alpha, 17.6% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'E' and resid 27 through 50 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.549A pdb=" N ILE E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 216 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 354 through 370 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 422 through 429 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O GLN E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 447 Processing helix chain 'E' and resid 455 through 466 removed outlier: 4.670A pdb=" N THR E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Proline residue: E 461 - end of helix removed outlier: 4.164A pdb=" N PHE E 464 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 488 Processing helix chain 'E' and resid 488 through 498 removed outlier: 3.517A pdb=" N PHE E 492 " --> pdb=" O TYR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 510 Processing helix chain 'E' and resid 511 through 527 Processing helix chain 'E' and resid 577 through 598 Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 603 through 607 Processing helix chain 'E' and resid 609 through 627 Processing helix chain 'E' and resid 643 through 653 Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 693 through 706 removed outlier: 3.770A pdb=" N ASN E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 747 Processing helix chain 'E' and resid 769 through 798 removed outlier: 3.974A pdb=" N ILE E 798 " --> pdb=" O ASN E 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 834 removed outlier: 3.523A pdb=" N LYS E 810 " --> pdb=" O ARG E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 843 through 869 removed outlier: 3.633A pdb=" N ILE E 849 " --> pdb=" O GLU E 845 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG E 867 " --> pdb=" O ALA E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 919 removed outlier: 3.967A pdb=" N LEU E 910 " --> pdb=" O PRO E 906 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 913 " --> pdb=" O MET E 909 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 919 " --> pdb=" O HIS E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1003 Processing helix chain 'E' and resid 1004 through 1008 Processing helix chain 'E' and resid 1011 through 1032 removed outlier: 3.709A pdb=" N VAL E1022 " --> pdb=" O ALA E1018 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1047 Processing helix chain 'E' and resid 1055 through 1060 removed outlier: 3.750A pdb=" N GLU E1060 " --> pdb=" O LYS E1057 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1078 Processing helix chain 'E' and resid 1079 through 1083 Processing helix chain 'E' and resid 1110 through 1114 Processing helix chain 'E' and resid 1115 through 1128 Processing helix chain 'E' and resid 1136 through 1141 Processing helix chain 'E' and resid 1142 through 1158 Processing helix chain 'E' and resid 1158 through 1165 Processing helix chain 'E' and resid 1177 through 1184 Processing sheet with id=AA1, first strand: chain 'E' and resid 75 through 78 removed outlier: 3.746A pdb=" N ARG E 75 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP E 264 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 81 through 87 removed outlier: 3.525A pdb=" N PHE E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 166 through 172 removed outlier: 6.889A pdb=" N THR E 187 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS E 143 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 241 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.869A pdb=" N GLY E 319 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE E 350 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU E 321 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU E 352 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR E 323 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET E 309 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU E 292 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE E 311 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP E 290 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR E 313 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 288 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 315 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 286 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET E 287 " --> pdb=" O SER E 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE E 374 " --> pdb=" O MET E 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AA6, first strand: chain 'E' and resid 542 through 543 Processing sheet with id=AA7, first strand: chain 'E' and resid 558 through 560 removed outlier: 6.926A pdb=" N TRP E 880 " --> pdb=" O LEU E 872 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU E 874 " --> pdb=" O GLY E 878 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 636 " --> pdb=" O PRO E 949 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 564 through 567 Processing sheet with id=AA9, first strand: chain 'E' and resid 572 through 575 Processing sheet with id=AB1, first strand: chain 'E' and resid 708 through 710 Processing sheet with id=AB2, first strand: chain 'E' and resid 890 through 894 Processing sheet with id=AB3, first strand: chain 'E' and resid 920 through 928 removed outlier: 4.044A pdb=" N GLN E 922 " --> pdb=" O HIS E 937 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS E 937 " --> pdb=" O GLN E 922 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN E 924 " --> pdb=" O GLU E 935 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU E 935 " --> pdb=" O GLN E 924 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU E 926 " --> pdb=" O ILE E 933 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE E 933 " --> pdb=" O LEU E 926 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 991 through 992 removed outlier: 4.049A pdb=" N ASN E1049 " --> pdb=" O GLU E 991 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 3464 1.40 - 1.62: 6138 1.62 - 1.83: 72 1.83 - 2.05: 0 2.05 - 2.27: 12 Bond restraints: 9686 Sorted by residual: bond pdb=" C PRO E 949 " pdb=" N TYR E 950 " ideal model delta sigma weight residual 1.331 1.563 -0.232 1.30e-02 5.92e+03 3.18e+02 bond pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 1.331 1.555 -0.224 2.07e-02 2.33e+03 1.18e+02 bond pdb=" N ILE E1107 " pdb=" CA ILE E1107 " ideal model delta sigma weight residual 1.462 1.403 0.059 1.01e-02 9.80e+03 3.36e+01 bond pdb=" C ASN E1169 " pdb=" N PRO E1170 " ideal model delta sigma weight residual 1.337 1.397 -0.061 1.11e-02 8.12e+03 2.99e+01 bond pdb=" C1' DG P 3 " pdb=" N9 DG P 3 " ideal model delta sigma weight residual 1.460 1.352 0.108 2.00e-02 2.50e+03 2.92e+01 ... (remaining 9681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 11829 2.81 - 5.62: 1284 5.62 - 8.43: 71 8.43 - 11.24: 13 11.24 - 14.04: 5 Bond angle restraints: 13202 Sorted by residual: angle pdb=" O GLU E 766 " pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 122.95 111.71 11.24 1.24e+00 6.50e-01 8.21e+01 angle pdb=" N LEU E 122 " pdb=" CA LEU E 122 " pdb=" C LEU E 122 " ideal model delta sigma weight residual 111.75 100.75 11.00 1.28e+00 6.10e-01 7.38e+01 angle pdb=" N PRO E 656 " pdb=" CA PRO E 656 " pdb=" C PRO E 656 " ideal model delta sigma weight residual 114.98 103.71 11.27 1.46e+00 4.69e-01 5.96e+01 angle pdb=" CA ASP E 151 " pdb=" CB ASP E 151 " pdb=" CG ASP E 151 " ideal model delta sigma weight residual 112.60 120.19 -7.59 1.00e+00 1.00e+00 5.76e+01 angle pdb=" C LYS E 751 " pdb=" CA LYS E 751 " pdb=" CB LYS E 751 " ideal model delta sigma weight residual 112.09 102.10 9.99 1.43e+00 4.89e-01 4.88e+01 ... (remaining 13197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5142 16.90 - 33.81: 450 33.81 - 50.71: 136 50.71 - 67.62: 54 67.62 - 84.52: 10 Dihedral angle restraints: 5792 sinusoidal: 2496 harmonic: 3296 Sorted by residual: dihedral pdb=" CA ARG E 749 " pdb=" C ARG E 749 " pdb=" N VAL E 750 " pdb=" CA VAL E 750 " ideal model delta harmonic sigma weight residual -180.00 -139.78 -40.22 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ARG E 672 " pdb=" C ARG E 672 " pdb=" N PRO E 673 " pdb=" CA PRO E 673 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO E 634 " pdb=" C PRO E 634 " pdb=" N LEU E 635 " pdb=" CA LEU E 635 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 5789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1182 0.125 - 0.249: 219 0.249 - 0.374: 29 0.374 - 0.499: 4 0.499 - 0.624: 7 Chirality restraints: 1441 Sorted by residual: chirality pdb=" P DC P 1 " pdb=" OP1 DC P 1 " pdb=" OP2 DC P 1 " pdb=" O5' DC P 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" P DT T 3 " pdb=" OP1 DT T 3 " pdb=" OP2 DT T 3 " pdb=" O5' DT T 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" P DG P 6 " pdb=" OP1 DG P 6 " pdb=" OP2 DG P 6 " pdb=" O5' DG P 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.54e+00 ... (remaining 1438 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 81 " -0.052 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C ASN E 81 " 0.179 2.00e-02 2.50e+03 pdb=" O ASN E 81 " -0.070 2.00e-02 2.50e+03 pdb=" N MET E 82 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 949 " -0.046 2.00e-02 2.50e+03 9.21e-02 8.49e+01 pdb=" C PRO E 949 " 0.159 2.00e-02 2.50e+03 pdb=" O PRO E 949 " -0.067 2.00e-02 2.50e+03 pdb=" N TYR E 950 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 485 " -0.119 2.00e-02 2.50e+03 6.35e-02 8.07e+01 pdb=" CG TYR E 485 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 485 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR E 485 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 485 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 485 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR E 485 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 485 " -0.087 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 572 2.74 - 3.28: 9248 3.28 - 3.82: 15270 3.82 - 4.36: 20063 4.36 - 4.90: 31911 Nonbonded interactions: 77064 Sorted by model distance: nonbonded pdb=" O GLU E 845 " pdb=" N ALA E 847 " model vdw 2.205 3.120 nonbonded pdb=" O LEU E 815 " pdb=" OG SER E 818 " model vdw 2.283 3.040 nonbonded pdb=" O GLU E 845 " pdb=" N GLY E 848 " model vdw 2.290 3.120 nonbonded pdb=" N ARG E 260 " pdb=" OH TYR E 265 " model vdw 2.291 3.120 nonbonded pdb=" O GLU E 124 " pdb=" N GLY E 126 " model vdw 2.296 3.120 ... (remaining 77059 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=1.00 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: 1.200 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5517 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 : 0.015 0.232 9686 Z= 0.929 Angle : 1.754 14.044 13202 Z= 1.157 Chirality : 0.106 0.624 1441 Planarity : 0.016 0.177 1628 Dihedral : 15.435 84.520 3662 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 1.08 % Allowed : 4.31 % Favored : 94.61 % Rotamer: Outliers : 2.06 % Allowed : 4.42 % Favored : 93.52 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.71 (0.23), residues: 1113 helix: -0.90 (0.21), residues: 459 sheet: -0.93 (0.35), residues: 197 loop : -1.29 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.016 TRP E 384 HIS 0.021 0.005 HIS E 388 PHE 0.071 0.010 PHE E 347 TYR 0.119 0.018 TYR E 485 ARG 0.017 0.002 ARG E 781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4688 (t80) REVERT: E 86 LEU cc_start: 0.8801 (tp) cc_final: 0.8513 (mp) REVERT: E 242 ILE cc_start: 0.8427 (pt) cc_final: 0.8189 (mt) REVERT: E 265 TYR cc_start: 0.6297 (m-80) cc_final: 0.5526 (m-80) REVERT: E 604 VAL cc_start: 0.6580 (m) cc_final: 0.6207 (m) REVERT: E 645 TYR cc_start: 0.7523 (m-10) cc_final: 0.7167 (m-10) REVERT: E 926 LEU cc_start: 0.6822 (tt) cc_final: 0.6606 (tp) outliers start: 20 outliers final: 3 residues processed: 313 average time/residue: 0.2578 time to fit residues: 105.5663 Evaluate side-chains 160 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 689 PHE Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 1038 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 HIS E 211 GLN E 572 ASN E 794 ASN E 823 HIS E1062 GLN E1176 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.164702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132951 restraints weight = 19709.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136551 restraints weight = 9749.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.138911 restraints weight = 6329.169| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9686 Z= 0.244 Angle : 0.692 9.543 13202 Z= 0.372 Chirality : 0.045 0.232 1441 Planarity : 0.005 0.064 1628 Dihedral : 13.702 77.966 1463 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 2.98 % Allowed : 13.07 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.29 (0.25), residues: 1113 helix: 1.05 (0.24), residues: 473 sheet: -0.26 (0.35), residues: 194 loop : -0.41 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E1143 HIS 0.005 0.001 HIS E 388 PHE 0.026 0.002 PHE E 830 TYR 0.016 0.002 TYR E 412 ARG 0.006 0.001 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.5125 (t80) REVERT: E 265 TYR cc_start: 0.6890 (m-80) cc_final: 0.6321 (m-80) REVERT: E 957 SER cc_start: 0.7919 (t) cc_final: 0.7622 (p) outliers start: 29 outliers final: 17 residues processed: 180 average time/residue: 0.2239 time to fit residues: 55.6989 Evaluate side-chains 140 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 68 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 ASN E 627 ASN E 924 GLN ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.152959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122225 restraints weight = 20186.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.124538 restraints weight = 10296.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126051 restraints weight = 6853.856| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9686 Z= 0.354 Angle : 0.726 10.501 13202 Z= 0.387 Chirality : 0.047 0.179 1441 Planarity : 0.006 0.104 1628 Dihedral : 13.498 65.700 1456 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 4.01 % Allowed : 15.74 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.26 (0.25), residues: 1113 helix: 0.90 (0.24), residues: 483 sheet: -0.21 (0.35), residues: 192 loop : -0.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 683 HIS 0.006 0.002 HIS E 823 PHE 0.021 0.002 PHE E 784 TYR 0.021 0.002 TYR E 833 ARG 0.005 0.001 ARG E 653 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.5305 (t80) REVERT: E 381 PHE cc_start: 0.7471 (t80) cc_final: 0.7163 (t80) REVERT: E 904 SER cc_start: 0.8561 (t) cc_final: 0.8228 (p) REVERT: E 957 SER cc_start: 0.8269 (t) cc_final: 0.7911 (p) REVERT: E 968 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7522 (mtp85) REVERT: E 1052 MET cc_start: 0.5891 (mtp) cc_final: 0.5518 (mtm) REVERT: E 1087 LEU cc_start: 0.4963 (tt) cc_final: 0.4252 (mt) REVERT: E 1091 TYR cc_start: 0.6385 (p90) cc_final: 0.6034 (p90) outliers start: 39 outliers final: 25 residues processed: 159 average time/residue: 0.2749 time to fit residues: 62.5865 Evaluate side-chains 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 417 CYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 571 LYS Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 857 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 954 ILE Chi-restraints excluded: chain E residue 1021 SER Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 924 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.154765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124697 restraints weight = 20078.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126474 restraints weight = 10097.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.129001 restraints weight = 7056.620| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9686 Z= 0.185 Angle : 0.610 7.829 13202 Z= 0.322 Chirality : 0.042 0.188 1441 Planarity : 0.004 0.073 1628 Dihedral : 13.250 66.377 1456 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.88 % Allowed : 17.08 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.75 (0.26), residues: 1113 helix: 1.33 (0.24), residues: 478 sheet: -0.14 (0.34), residues: 200 loop : 0.03 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1143 HIS 0.003 0.001 HIS E 546 PHE 0.015 0.001 PHE E 984 TYR 0.017 0.001 TYR E 742 ARG 0.003 0.000 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5547 (OUTLIER) cc_final: 0.5214 (t80) REVERT: E 265 TYR cc_start: 0.7524 (m-80) cc_final: 0.7229 (m-80) REVERT: E 517 GLU cc_start: 0.8127 (tp30) cc_final: 0.7875 (tp30) REVERT: E 783 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7880 (tm-30) REVERT: E 787 LEU cc_start: 0.7773 (tp) cc_final: 0.7383 (mt) REVERT: E 904 SER cc_start: 0.8531 (t) cc_final: 0.8172 (p) REVERT: E 957 SER cc_start: 0.8263 (t) cc_final: 0.7858 (p) REVERT: E 1042 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7862 (tt) REVERT: E 1087 LEU cc_start: 0.4624 (tt) cc_final: 0.4019 (mt) outliers start: 28 outliers final: 16 residues processed: 145 average time/residue: 0.2696 time to fit residues: 56.3985 Evaluate side-chains 123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 0.0770 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3144 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.150643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118942 restraints weight = 20133.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122042 restraints weight = 10231.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.124006 restraints weight = 6817.407| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9686 Z= 0.265 Angle : 0.625 8.168 13202 Z= 0.328 Chirality : 0.043 0.162 1441 Planarity : 0.004 0.078 1628 Dihedral : 13.159 70.991 1456 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.70 % Allowed : 17.28 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.26), residues: 1113 helix: 1.40 (0.24), residues: 477 sheet: -0.07 (0.35), residues: 203 loop : -0.05 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E1026 HIS 0.005 0.001 HIS E 250 PHE 0.016 0.002 PHE E1122 TYR 0.015 0.002 TYR E 833 ARG 0.005 0.001 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5351 (t80) REVERT: E 783 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7819 (tm-30) REVERT: E 787 LEU cc_start: 0.7769 (tp) cc_final: 0.7439 (mt) REVERT: E 904 SER cc_start: 0.8571 (t) cc_final: 0.8208 (p) REVERT: E 955 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7456 (mp) REVERT: E 957 SER cc_start: 0.8416 (t) cc_final: 0.8088 (p) REVERT: E 968 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7869 (mtt90) REVERT: E 1042 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7930 (tt) REVERT: E 1087 LEU cc_start: 0.4863 (tt) cc_final: 0.4364 (mt) REVERT: E 1091 TYR cc_start: 0.6517 (p90) cc_final: 0.6186 (p90) outliers start: 36 outliers final: 23 residues processed: 139 average time/residue: 0.2085 time to fit residues: 41.7710 Evaluate side-chains 127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1029 VAL Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.153831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124491 restraints weight = 20103.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126225 restraints weight = 10079.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128070 restraints weight = 7002.062| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9686 Z= 0.165 Angle : 0.572 6.898 13202 Z= 0.299 Chirality : 0.041 0.172 1441 Planarity : 0.004 0.055 1628 Dihedral : 13.074 71.296 1456 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.37 % Allowed : 19.86 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.03 (0.26), residues: 1113 helix: 1.63 (0.24), residues: 476 sheet: 0.09 (0.36), residues: 190 loop : 0.04 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 841 HIS 0.002 0.000 HIS E 937 PHE 0.019 0.001 PHE E 984 TYR 0.029 0.002 TYR E 449 ARG 0.005 0.000 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.5210 (t80) REVERT: E 265 TYR cc_start: 0.7549 (m-80) cc_final: 0.7348 (m-80) REVERT: E 517 GLU cc_start: 0.7713 (tp30) cc_final: 0.7498 (tp30) REVERT: E 783 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7769 (tm-30) REVERT: E 787 LEU cc_start: 0.7854 (tp) cc_final: 0.7499 (mt) REVERT: E 904 SER cc_start: 0.8670 (t) cc_final: 0.8427 (p) REVERT: E 957 SER cc_start: 0.8374 (t) cc_final: 0.8024 (p) REVERT: E 1042 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7995 (tp) REVERT: E 1091 TYR cc_start: 0.6408 (p90) cc_final: 0.6104 (p90) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 0.2014 time to fit residues: 36.9329 Evaluate side-chains 120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.154348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.124753 restraints weight = 20439.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.126409 restraints weight = 10388.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128085 restraints weight = 7184.933| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9686 Z= 0.169 Angle : 0.587 10.426 13202 Z= 0.299 Chirality : 0.041 0.157 1441 Planarity : 0.004 0.059 1628 Dihedral : 13.006 75.099 1456 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.09 % Allowed : 19.34 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.16 (0.26), residues: 1113 helix: 1.76 (0.24), residues: 472 sheet: 0.05 (0.35), residues: 198 loop : 0.16 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1143 HIS 0.003 0.001 HIS E 469 PHE 0.011 0.001 PHE E1122 TYR 0.025 0.001 TYR E 449 ARG 0.006 0.000 ARG E 968 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.5216 (t80) REVERT: E 517 GLU cc_start: 0.7759 (tp30) cc_final: 0.7421 (tp30) REVERT: E 644 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7578 (ttm) REVERT: E 904 SER cc_start: 0.8629 (t) cc_final: 0.8376 (p) REVERT: E 957 SER cc_start: 0.8415 (t) cc_final: 0.8077 (p) REVERT: E 1091 TYR cc_start: 0.6343 (p90) cc_final: 0.6083 (p90) outliers start: 30 outliers final: 20 residues processed: 131 average time/residue: 0.2007 time to fit residues: 38.1601 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 644 MET Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117831 restraints weight = 20742.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120902 restraints weight = 10480.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.122844 restraints weight = 6967.967| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9686 Z= 0.295 Angle : 0.646 10.227 13202 Z= 0.333 Chirality : 0.044 0.163 1441 Planarity : 0.004 0.056 1628 Dihedral : 13.010 74.357 1456 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.09 % Allowed : 19.96 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.26), residues: 1113 helix: 1.58 (0.24), residues: 472 sheet: -0.06 (0.36), residues: 197 loop : 0.05 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 791 HIS 0.005 0.001 HIS E 250 PHE 0.016 0.002 PHE E1122 TYR 0.025 0.002 TYR E 449 ARG 0.004 0.001 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.5248 (t80) REVERT: E 955 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7493 (mp) REVERT: E 957 SER cc_start: 0.8487 (t) cc_final: 0.8115 (p) REVERT: E 1087 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4343 (mt) REVERT: E 1091 TYR cc_start: 0.6749 (p90) cc_final: 0.6525 (p90) REVERT: E 1164 LEU cc_start: 0.8464 (pp) cc_final: 0.7919 (mt) outliers start: 30 outliers final: 23 residues processed: 132 average time/residue: 0.1975 time to fit residues: 37.7211 Evaluate side-chains 127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 827 LEU Chi-restraints excluded: chain E residue 857 ILE Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1082 VAL Chi-restraints excluded: chain E residue 1087 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.152259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120818 restraints weight = 20354.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.123953 restraints weight = 10285.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125921 restraints weight = 6829.305| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9686 Z= 0.179 Angle : 0.601 9.591 13202 Z= 0.310 Chirality : 0.042 0.156 1441 Planarity : 0.004 0.052 1628 Dihedral : 12.983 73.469 1456 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.06 % Allowed : 21.19 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.01 (0.26), residues: 1113 helix: 1.61 (0.24), residues: 471 sheet: 0.00 (0.36), residues: 197 loop : 0.09 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 841 HIS 0.002 0.001 HIS E 921 PHE 0.012 0.001 PHE E 193 TYR 0.022 0.001 TYR E 449 ARG 0.006 0.000 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.5287 (t80) REVERT: E 957 SER cc_start: 0.8471 (t) cc_final: 0.8123 (p) REVERT: E 1091 TYR cc_start: 0.6564 (p90) cc_final: 0.6357 (p90) REVERT: E 1164 LEU cc_start: 0.8452 (pp) cc_final: 0.7874 (mt) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.2176 time to fit residues: 39.7355 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1082 VAL Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.119216 restraints weight = 20788.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120867 restraints weight = 10638.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122192 restraints weight = 7688.764| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9686 Z= 0.271 Angle : 0.664 16.970 13202 Z= 0.337 Chirality : 0.044 0.158 1441 Planarity : 0.004 0.058 1628 Dihedral : 13.033 74.054 1456 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.37 % Allowed : 21.19 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.80 (0.26), residues: 1113 helix: 1.45 (0.24), residues: 470 sheet: -0.08 (0.36), residues: 197 loop : -0.05 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 791 HIS 0.005 0.001 HIS E 250 PHE 0.016 0.002 PHE E 193 TYR 0.023 0.002 TYR E 449 ARG 0.006 0.001 ARG E 968 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.5156 (t80) REVERT: E 381 PHE cc_start: 0.7273 (t80) cc_final: 0.6990 (t80) REVERT: E 466 LYS cc_start: 0.7633 (mttt) cc_final: 0.7080 (tptp) REVERT: E 957 SER cc_start: 0.8514 (t) cc_final: 0.8150 (p) REVERT: E 1036 MET cc_start: 0.7324 (mmm) cc_final: 0.6639 (mmp) REVERT: E 1087 LEU cc_start: 0.4458 (tt) cc_final: 0.4170 (mt) REVERT: E 1091 TYR cc_start: 0.6749 (p90) cc_final: 0.6520 (p90) REVERT: E 1126 TRP cc_start: 0.4277 (m-10) cc_final: 0.2387 (m-10) REVERT: E 1164 LEU cc_start: 0.8506 (pp) cc_final: 0.7858 (mt) outliers start: 23 outliers final: 21 residues processed: 133 average time/residue: 0.2127 time to fit residues: 40.4915 Evaluate side-chains 126 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1029 VAL Chi-restraints excluded: chain E residue 1082 VAL Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.0470 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.151858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.121538 restraints weight = 20676.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124368 restraints weight = 11253.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124844 restraints weight = 7215.525| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9686 Z= 0.188 Angle : 0.622 13.442 13202 Z= 0.314 Chirality : 0.042 0.156 1441 Planarity : 0.004 0.050 1628 Dihedral : 13.075 74.829 1456 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.16 % Allowed : 21.81 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.96 (0.26), residues: 1113 helix: 1.59 (0.24), residues: 471 sheet: -0.02 (0.36), residues: 197 loop : 0.04 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 841 HIS 0.002 0.001 HIS E 921 PHE 0.012 0.001 PHE E 193 TYR 0.020 0.001 TYR E 449 ARG 0.006 0.000 ARG E 968 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.93 seconds wall clock time: 58 minutes 34.67 seconds (3514.67 seconds total)