Starting phenix.real_space_refine on Thu Jan 16 10:11:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8r_44356/01_2025/9b8r_44356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8r_44356/01_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_44356/01_2025/9b8r_44356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8r_44356/01_2025/9b8r_44356.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8r_44356/01_2025/9b8r_44356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8r_44356/01_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-5571/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: 5.92, per 1000 atoms: 0.63 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.52 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: 4.33 Time building geometry restraints manager: 2.88 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: 1.070 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.590 Find NCS groups from input model: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- 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 : 0.997 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: 0.2789 time to fit residues: 114.0642 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 : 1.034 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133003 restraints weight = 19709.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.136596 restraints weight = 9715.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138958 restraints weight = 6267.729| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5408 (OUTLIER) cc_final: 0.5123 (t80) REVERT: E 265 TYR cc_start: 0.6886 (m-80) cc_final: 0.6317 (m-80) REVERT: E 957 SER cc_start: 0.7918 (t) cc_final: 0.7628 (p) outliers start: 29 outliers final: 17 residues processed: 180 average time/residue: 0.2396 time to fit residues: 59.1250 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 : 1.117 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.9980 chunk 68 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 ASN E 572 ASN E 627 ASN E 924 GLN ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.153180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122466 restraints weight = 20160.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.125243 restraints weight = 10323.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126124 restraints weight = 7084.296| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9686 Z= 0.358 Angle : 0.724 10.193 13202 Z= 0.385 Chirality : 0.046 0.176 1441 Planarity : 0.006 0.097 1628 Dihedral : 13.481 65.665 1456 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 3.70 % Allowed : 15.74 % Favored : 80.56 % 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: 0.27 (0.25), residues: 1113 helix: 0.92 (0.24), residues: 483 sheet: -0.21 (0.35), residues: 192 loop : -0.33 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 683 HIS 0.006 0.002 HIS E1176 PHE 0.020 0.002 PHE E 784 TYR 0.018 0.002 TYR E 462 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 164 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5650 (OUTLIER) cc_final: 0.5340 (t80) REVERT: E 381 PHE cc_start: 0.7467 (t80) cc_final: 0.7167 (t80) REVERT: E 904 SER cc_start: 0.8562 (t) cc_final: 0.8226 (p) REVERT: E 957 SER cc_start: 0.8263 (t) cc_final: 0.7894 (p) REVERT: E 968 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7553 (mtp85) REVERT: E 1087 LEU cc_start: 0.4988 (tt) cc_final: 0.4455 (mt) REVERT: E 1091 TYR cc_start: 0.6378 (p90) cc_final: 0.6011 (p90) outliers start: 36 outliers final: 24 residues processed: 158 average time/residue: 0.2192 time to fit residues: 48.7089 Evaluate side-chains 127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 413 LYS 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 879 ILE Chi-restraints excluded: chain E residue 954 ILE 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: 0.7980 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 924 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.155621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.125559 restraints weight = 19907.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128187 restraints weight = 9886.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129213 restraints weight = 6928.089| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5353 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= 0.173 Angle : 0.606 8.169 13202 Z= 0.319 Chirality : 0.042 0.173 1441 Planarity : 0.004 0.064 1628 Dihedral : 13.241 66.365 1456 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.16 % Allowed : 17.59 % Favored : 80.25 % 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: 0.79 (0.26), residues: 1113 helix: 1.37 (0.24), residues: 478 sheet: -0.16 (0.34), residues: 200 loop : 0.06 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1026 HIS 0.003 0.001 HIS E 546 PHE 0.018 0.001 PHE E 984 TYR 0.018 0.001 TYR E 742 ARG 0.006 0.001 ARG E 988 *********************** 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 142 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.5167 (t80) REVERT: E 265 TYR cc_start: 0.7486 (m-80) cc_final: 0.7211 (m-80) REVERT: E 517 GLU cc_start: 0.8133 (tp30) cc_final: 0.7916 (tp30) REVERT: E 783 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 787 LEU cc_start: 0.7718 (tp) cc_final: 0.7355 (mt) REVERT: E 904 SER cc_start: 0.8485 (t) cc_final: 0.8117 (p) REVERT: E 957 SER cc_start: 0.8209 (t) cc_final: 0.7863 (p) REVERT: E 968 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7657 (mtt90) REVERT: E 1042 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7853 (tt) REVERT: E 1087 LEU cc_start: 0.4660 (tt) cc_final: 0.4054 (mt) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 0.2169 time to fit residues: 42.1098 Evaluate side-chains 122 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 49 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 413 LYS 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 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: 8.9990 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.151499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.119798 restraints weight = 20050.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122920 restraints weight = 10191.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124888 restraints weight = 6754.558| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5858 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= 0.245 Angle : 0.616 9.343 13202 Z= 0.320 Chirality : 0.043 0.157 1441 Planarity : 0.005 0.093 1628 Dihedral : 13.135 70.639 1456 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 0.86 (0.26), residues: 1113 helix: 1.45 (0.24), residues: 477 sheet: -0.11 (0.36), residues: 195 loop : 0.04 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 841 HIS 0.004 0.001 HIS E 250 PHE 0.019 0.002 PHE E 984 TYR 0.012 0.002 TYR E 833 ARG 0.008 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 150 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.040 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: 0.5729 (OUTLIER) cc_final: 0.5372 (t80) REVERT: E 783 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7826 (tm-30) REVERT: E 787 LEU cc_start: 0.7845 (tp) cc_final: 0.7500 (mt) REVERT: E 904 SER cc_start: 0.8561 (t) cc_final: 0.8194 (p) REVERT: E 955 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7447 (mp) REVERT: E 957 SER cc_start: 0.8383 (t) cc_final: 0.8071 (p) REVERT: E 1042 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7899 (tt) REVERT: E 1087 LEU cc_start: 0.4820 (tt) cc_final: 0.4326 (mt) REVERT: E 1091 TYR cc_start: 0.6459 (p90) cc_final: 0.6130 (p90) outliers start: 36 outliers final: 22 residues processed: 142 average time/residue: 0.2021 time to fit residues: 41.3688 Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 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 561 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 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: 5.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 106 optimal weight: 0.0000 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120321 restraints weight = 20031.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123470 restraints weight = 10118.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125380 restraints weight = 6697.618| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6080 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= 0.200 Angle : 0.587 7.707 13202 Z= 0.306 Chirality : 0.042 0.160 1441 Planarity : 0.004 0.075 1628 Dihedral : 13.084 70.148 1456 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.09 % Allowed : 18.21 % Favored : 78.70 % 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: 1.68 (0.24), residues: 470 sheet: -0.05 (0.36), residues: 195 loop : 0.04 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1143 HIS 0.003 0.001 HIS E 250 PHE 0.012 0.001 PHE E1122 TYR 0.029 0.002 TYR E 449 ARG 0.004 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 139 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.113 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: 0.5609 (OUTLIER) cc_final: 0.5244 (t80) REVERT: E 783 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7799 (tm-30) REVERT: E 787 LEU cc_start: 0.7821 (tp) cc_final: 0.7477 (mt) REVERT: E 904 SER cc_start: 0.8602 (t) cc_final: 0.8392 (p) REVERT: E 957 SER cc_start: 0.8368 (t) cc_final: 0.8048 (p) REVERT: E 1042 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7952 (tt) REVERT: E 1087 LEU cc_start: 0.4588 (tt) cc_final: 0.4134 (mt) REVERT: E 1091 TYR cc_start: 0.6543 (p90) cc_final: 0.6258 (p90) outliers start: 30 outliers final: 22 residues processed: 131 average time/residue: 0.2267 time to fit residues: 42.3336 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 49 MET Chi-restraints excluded: chain E residue 70 ASP 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 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 413 LYS 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 941 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.154463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.124593 restraints weight = 20261.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.126861 restraints weight = 11028.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127740 restraints weight = 7167.809| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9686 Z= 0.161 Angle : 0.582 10.907 13202 Z= 0.298 Chirality : 0.041 0.153 1441 Planarity : 0.004 0.066 1628 Dihedral : 13.033 73.589 1456 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.78 % Allowed : 18.83 % Favored : 78.40 % 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: 1.15 (0.26), residues: 1113 helix: 1.75 (0.24), residues: 471 sheet: 0.10 (0.36), residues: 192 loop : 0.11 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 841 HIS 0.003 0.001 HIS E 469 PHE 0.010 0.001 PHE E1112 TYR 0.025 0.001 TYR E 449 ARG 0.004 0.000 ARG E 428 *********************** 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 138 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5493 (OUTLIER) cc_final: 0.5166 (t80) REVERT: E 310 MET cc_start: 0.7309 (ttm) cc_final: 0.7052 (ttp) REVERT: E 644 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7267 (ttm) REVERT: E 783 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7759 (tm-30) REVERT: E 787 LEU cc_start: 0.7840 (tp) cc_final: 0.7514 (mt) REVERT: E 870 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.7949 (ttp-110) REVERT: E 904 SER cc_start: 0.8655 (t) cc_final: 0.8410 (p) REVERT: E 955 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7431 (mp) REVERT: E 957 SER cc_start: 0.8390 (t) cc_final: 0.8041 (p) REVERT: E 1087 LEU cc_start: 0.4147 (tt) cc_final: 0.3809 (mt) REVERT: E 1091 TYR cc_start: 0.6381 (p90) cc_final: 0.6112 (p90) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.2104 time to fit residues: 39.6905 Evaluate side-chains 127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 369 VAL Chi-restraints excluded: chain E residue 413 LYS 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 644 MET Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 101 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.152985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.123078 restraints weight = 20457.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125380 restraints weight = 11163.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125967 restraints weight = 7209.586| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9686 Z= 0.189 Angle : 0.592 10.261 13202 Z= 0.303 Chirality : 0.042 0.151 1441 Planarity : 0.004 0.066 1628 Dihedral : 12.981 74.485 1456 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.37 % Allowed : 19.55 % Favored : 78.09 % 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: 1.14 (0.26), residues: 1113 helix: 1.74 (0.24), residues: 471 sheet: 0.07 (0.36), residues: 198 loop : 0.13 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1143 HIS 0.003 0.001 HIS E 250 PHE 0.013 0.001 PHE E 918 TYR 0.022 0.001 TYR E 449 ARG 0.005 0.000 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 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.143 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: 0.5194 (t80) REVERT: E 310 MET cc_start: 0.7286 (ttm) cc_final: 0.7028 (ttp) REVERT: E 791 TRP cc_start: 0.7174 (m100) cc_final: 0.6943 (m100) REVERT: E 844 MET cc_start: 0.7222 (tpp) cc_final: 0.6725 (tpp) REVERT: E 904 SER cc_start: 0.8609 (t) cc_final: 0.8387 (p) REVERT: E 957 SER cc_start: 0.8409 (t) cc_final: 0.8075 (p) REVERT: E 1087 LEU cc_start: 0.4145 (tt) cc_final: 0.3847 (mt) REVERT: E 1091 TYR cc_start: 0.6486 (p90) cc_final: 0.6240 (p90) outliers start: 23 outliers final: 20 residues processed: 129 average time/residue: 0.2231 time to fit residues: 40.8136 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 369 VAL Chi-restraints excluded: chain E residue 413 LYS 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 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 32 optimal weight: 0.0370 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.154463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123111 restraints weight = 20326.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.126248 restraints weight = 10248.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128227 restraints weight = 6808.438| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9686 Z= 0.159 Angle : 0.577 9.836 13202 Z= 0.295 Chirality : 0.041 0.157 1441 Planarity : 0.004 0.059 1628 Dihedral : 12.986 74.134 1456 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.16 % Allowed : 20.06 % 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: 1.19 (0.26), residues: 1113 helix: 1.84 (0.24), residues: 469 sheet: 0.04 (0.36), residues: 199 loop : 0.12 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 841 HIS 0.002 0.000 HIS E 921 PHE 0.015 0.001 PHE E 193 TYR 0.021 0.001 TYR E 449 ARG 0.003 0.000 ARG E 989 *********************** 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 127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.168 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: 0.5688 (OUTLIER) cc_final: 0.5293 (t80) REVERT: E 310 MET cc_start: 0.7277 (ttm) cc_final: 0.7000 (ttp) REVERT: E 644 MET cc_start: 0.8001 (tpp) cc_final: 0.7388 (ttm) REVERT: E 904 SER cc_start: 0.8465 (t) cc_final: 0.8238 (p) REVERT: E 957 SER cc_start: 0.8438 (t) cc_final: 0.8111 (p) outliers start: 21 outliers final: 19 residues processed: 122 average time/residue: 0.2006 time to fit residues: 36.1716 Evaluate side-chains 123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.153898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122324 restraints weight = 20647.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125516 restraints weight = 10298.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127539 restraints weight = 6788.935| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9686 Z= 0.170 Angle : 0.582 9.805 13202 Z= 0.297 Chirality : 0.042 0.156 1441 Planarity : 0.004 0.094 1628 Dihedral : 13.058 75.646 1456 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.26 % Allowed : 20.27 % Favored : 77.47 % 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: 1.14 (0.26), residues: 1113 helix: 1.76 (0.24), residues: 470 sheet: 0.04 (0.36), residues: 199 loop : 0.13 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 791 HIS 0.002 0.001 HIS E 250 PHE 0.016 0.001 PHE E 193 TYR 0.019 0.001 TYR E 449 ARG 0.004 0.000 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 132 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.5333 (t80) REVERT: E 310 MET cc_start: 0.7273 (ttm) cc_final: 0.6999 (ttp) REVERT: E 644 MET cc_start: 0.8025 (tpp) cc_final: 0.7405 (ttm) REVERT: E 904 SER cc_start: 0.8492 (t) cc_final: 0.8287 (p) REVERT: E 957 SER cc_start: 0.8434 (t) cc_final: 0.8091 (p) REVERT: E 1087 LEU cc_start: 0.4406 (tt) cc_final: 0.4102 (mt) outliers start: 22 outliers final: 21 residues processed: 128 average time/residue: 0.2158 time to fit residues: 40.1827 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 369 VAL Chi-restraints excluded: chain E residue 413 LYS 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 941 THR Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 0.0040 chunk 111 optimal weight: 0.0770 chunk 65 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 overall best weight: 1.3152 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.152527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121082 restraints weight = 20442.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.124223 restraints weight = 10231.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.126217 restraints weight = 6746.324| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6871 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= 0.192 Angle : 0.615 19.111 13202 Z= 0.307 Chirality : 0.042 0.153 1441 Planarity : 0.004 0.086 1628 Dihedral : 13.125 75.355 1456 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.37 % Allowed : 20.88 % 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: 1.10 (0.26), residues: 1113 helix: 1.72 (0.24), residues: 470 sheet: -0.01 (0.36), residues: 199 loop : 0.14 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 791 HIS 0.003 0.001 HIS E 419 PHE 0.019 0.001 PHE E 193 TYR 0.017 0.001 TYR E 449 ARG 0.004 0.000 ARG E 968 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.99 seconds wall clock time: 56 minutes 32.63 seconds (3392.63 seconds total)