Starting phenix.real_space_refine on Fri Nov 15 18:02:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8r_44356/11_2024/9b8r_44356.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8r_44356/11_2024/9b8r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8r_44356/11_2024/9b8r_44356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8r_44356/11_2024/9b8r_44356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8r_44356/11_2024/9b8r_44356.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8r_44356/11_2024/9b8r_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-5513/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: 5.43, per 1000 atoms: 0.58 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: 2.57 Conformation dependent library (CDL) restraints added in 1.0 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: 3.11 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: 4.31 Time building geometry restraints manager: 2.95 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: 0.870 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.920 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- 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 : 1.038 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: 0.2850 time to fit residues: 116.5532 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 : 1.137 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 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 : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5240 (OUTLIER) cc_final: 0.4903 (t80) REVERT: E 265 TYR cc_start: 0.6630 (m-80) cc_final: 0.6005 (m-80) REVERT: E 420 MET cc_start: 0.9367 (mmt) cc_final: 0.9151 (mmt) outliers start: 29 outliers final: 17 residues processed: 180 average time/residue: 0.2287 time to fit residues: 56.9825 Evaluate side-chains 139 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 57 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9686 Z= 0.192 Angle : 0.619 9.153 13202 Z= 0.329 Chirality : 0.043 0.161 1441 Planarity : 0.005 0.083 1628 Dihedral : 13.240 66.707 1456 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.98 % Favored : 97.93 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.30 % 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: 0.71 (0.26), residues: 1113 helix: 1.34 (0.24), residues: 473 sheet: -0.22 (0.35), residues: 202 loop : -0.01 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 683 HIS 0.003 0.001 HIS E 915 PHE 0.018 0.002 PHE E 984 TYR 0.012 0.001 TYR E 313 ARG 0.003 0.001 ARG E1138 *********************** 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 163 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.4912 (t80) REVERT: E 238 LEU cc_start: 0.7747 (mt) cc_final: 0.7535 (mt) REVERT: E 265 TYR cc_start: 0.6942 (m-80) cc_final: 0.6304 (m-80) REVERT: E 381 PHE cc_start: 0.7477 (t80) cc_final: 0.7127 (t80) REVERT: E 557 HIS cc_start: 0.7276 (t70) cc_final: 0.6936 (t70) REVERT: E 613 ILE cc_start: 0.8140 (mm) cc_final: 0.7744 (mt) REVERT: E 834 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8202 (p) REVERT: E 992 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5165 (tt) outliers start: 28 outliers final: 17 residues processed: 159 average time/residue: 0.2166 time to fit residues: 48.9604 Evaluate side-chains 131 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 246 ASP 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 418 SER Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 834 VAL Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 957 SER Chi-restraints excluded: chain E residue 992 LEU 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 101 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 ASN E1176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9686 Z= 0.273 Angle : 0.659 8.755 13202 Z= 0.346 Chirality : 0.044 0.199 1441 Planarity : 0.005 0.088 1628 Dihedral : 13.282 68.396 1456 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.50 % Allowed : 16.36 % Favored : 80.14 % 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: 0.71 (0.26), residues: 1113 helix: 1.33 (0.24), residues: 477 sheet: -0.28 (0.36), residues: 195 loop : 0.03 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 683 HIS 0.006 0.002 HIS E 546 PHE 0.017 0.002 PHE E1122 TYR 0.027 0.002 TYR E 833 ARG 0.008 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 155 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.5307 (t80) REVERT: E 381 PHE cc_start: 0.7549 (t80) cc_final: 0.7322 (t80) REVERT: E 904 SER cc_start: 0.8375 (t) cc_final: 0.8109 (p) REVERT: E 1042 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6509 (tt) outliers start: 34 outliers final: 25 residues processed: 147 average time/residue: 0.2163 time to fit residues: 45.0175 Evaluate side-chains 134 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 366 ILE 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 519 LEU 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 957 SER 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 62 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9686 Z= 0.176 Angle : 0.585 7.944 13202 Z= 0.304 Chirality : 0.042 0.154 1441 Planarity : 0.004 0.073 1628 Dihedral : 13.162 68.506 1456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.67 % Allowed : 17.28 % 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: 0.89 (0.26), residues: 1113 helix: 1.49 (0.24), residues: 477 sheet: -0.12 (0.36), residues: 192 loop : 0.07 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1026 HIS 0.002 0.001 HIS E 937 PHE 0.016 0.001 PHE E 984 TYR 0.016 0.001 TYR E 842 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 149 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.999 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: 0.5664 (OUTLIER) cc_final: 0.5236 (t80) REVERT: E 265 TYR cc_start: 0.7288 (m-80) cc_final: 0.6827 (m-80) REVERT: E 904 SER cc_start: 0.8355 (t) cc_final: 0.8095 (p) REVERT: E 1042 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6594 (tt) REVERT: E 1164 LEU cc_start: 0.7214 (pp) cc_final: 0.6480 (mt) outliers start: 26 outliers final: 16 residues processed: 143 average time/residue: 0.2002 time to fit residues: 41.2644 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 : 1.054 ------------------------------------------------------------------------------- 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 211 GLN 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 397 ASP Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 957 SER 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 98 optimal weight: 0.0020 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9686 Z= 0.174 Angle : 0.566 7.650 13202 Z= 0.294 Chirality : 0.041 0.160 1441 Planarity : 0.004 0.083 1628 Dihedral : 13.115 74.248 1456 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.98 % Allowed : 18.93 % 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: 1.08 (0.26), residues: 1113 helix: 1.65 (0.24), residues: 478 sheet: -0.01 (0.36), residues: 192 loop : 0.15 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1143 HIS 0.003 0.001 HIS E 823 PHE 0.019 0.001 PHE E 984 TYR 0.027 0.002 TYR E 449 ARG 0.006 0.001 ARG E 968 *********************** 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 141 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.012 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: 0.5782 (OUTLIER) cc_final: 0.5332 (t80) REVERT: E 904 SER cc_start: 0.8412 (t) cc_final: 0.8081 (p) REVERT: E 1042 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6673 (tt) REVERT: E 1164 LEU cc_start: 0.7255 (pp) cc_final: 0.6409 (mt) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 0.2027 time to fit residues: 39.8826 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 519 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 885 LYS Chi-restraints excluded: chain E residue 957 SER 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 12 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9686 Z= 0.402 Angle : 0.738 6.728 13202 Z= 0.389 Chirality : 0.048 0.178 1441 Planarity : 0.005 0.097 1628 Dihedral : 13.273 72.049 1456 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.09 % Allowed : 19.03 % Favored : 77.88 % 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: 0.51 (0.25), residues: 1113 helix: 1.22 (0.24), residues: 470 sheet: -0.26 (0.36), residues: 195 loop : -0.20 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E1026 HIS 0.008 0.002 HIS E 250 PHE 0.021 0.002 PHE E1122 TYR 0.022 0.002 TYR E 449 ARG 0.006 0.001 ARG E 361 *********************** 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 146 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.5326 (t80) REVERT: E 310 MET cc_start: 0.7848 (ptm) cc_final: 0.7619 (ptm) REVERT: E 381 PHE cc_start: 0.7515 (t80) cc_final: 0.7167 (t80) REVERT: E 506 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8254 (mt-10) REVERT: E 927 LYS cc_start: 0.8346 (tttt) cc_final: 0.7969 (pttt) REVERT: E 1042 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6830 (tt) REVERT: E 1158 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6698 (mt) outliers start: 30 outliers final: 22 residues processed: 140 average time/residue: 0.2250 time to fit residues: 44.7772 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 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 285 VAL Chi-restraints excluded: chain E residue 305 VAL 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 519 LEU Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 957 SER Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1092 ILE Chi-restraints excluded: chain E residue 1154 ILE Chi-restraints excluded: chain E residue 1158 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 65 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 104 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.6642 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= 0.169 Angle : 0.612 7.769 13202 Z= 0.318 Chirality : 0.042 0.159 1441 Planarity : 0.004 0.069 1628 Dihedral : 13.114 70.659 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 : 2.16 % Allowed : 20.88 % 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: 0.82 (0.26), residues: 1113 helix: 1.56 (0.24), residues: 475 sheet: -0.21 (0.36), residues: 197 loop : -0.10 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 841 HIS 0.002 0.001 HIS E 490 PHE 0.015 0.001 PHE E 139 TYR 0.024 0.002 TYR E 449 ARG 0.018 0.001 ARG E 806 *********************** 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: 21 poor density : 117 time to evaluate : 1.101 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: 0.5818 (OUTLIER) cc_final: 0.5365 (t80) REVERT: E 310 MET cc_start: 0.7786 (ptm) cc_final: 0.7577 (ptm) REVERT: E 507 THR cc_start: 0.8744 (m) cc_final: 0.8420 (p) REVERT: E 1164 LEU cc_start: 0.7097 (pp) cc_final: 0.6217 (mt) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.2198 time to fit residues: 41.6648 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 470 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 544 ASP Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 587 GLU Chi-restraints excluded: chain E residue 857 ILE Chi-restraints excluded: chain E residue 885 LYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 954 ILE Chi-restraints excluded: chain E residue 957 SER 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 101 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9686 Z= 0.306 Angle : 0.685 12.052 13202 Z= 0.352 Chirality : 0.045 0.165 1441 Planarity : 0.005 0.079 1628 Dihedral : 13.063 74.166 1456 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 2.88 % Allowed : 20.58 % Favored : 76.54 % 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: 0.73 (0.26), residues: 1113 helix: 1.47 (0.24), residues: 470 sheet: -0.27 (0.36), residues: 197 loop : -0.09 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 791 HIS 0.006 0.001 HIS E 250 PHE 0.017 0.002 PHE E1122 TYR 0.025 0.002 TYR E 449 ARG 0.006 0.001 ARG E 968 *********************** 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 137 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.5369 (t80) REVERT: E 70 ASP cc_start: 0.7973 (p0) cc_final: 0.7690 (m-30) REVERT: E 310 MET cc_start: 0.7851 (ptm) cc_final: 0.7632 (ptm) REVERT: E 381 PHE cc_start: 0.7562 (t80) cc_final: 0.7222 (t80) REVERT: E 506 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 507 THR cc_start: 0.8873 (m) cc_final: 0.8607 (p) REVERT: E 812 MET cc_start: 0.8774 (ttm) cc_final: 0.8566 (ttt) REVERT: E 927 LYS cc_start: 0.8334 (tttt) cc_final: 0.8052 (pttt) REVERT: E 1126 TRP cc_start: 0.3153 (m-10) cc_final: 0.1723 (m-10) outliers start: 28 outliers final: 27 residues processed: 130 average time/residue: 0.2315 time to fit residues: 42.4264 Evaluate side-chains 130 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 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 474 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 519 LEU Chi-restraints excluded: chain E residue 544 ASP Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 587 GLU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 857 ILE Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 954 ILE Chi-restraints excluded: chain E residue 957 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9686 Z= 0.194 Angle : 0.645 10.829 13202 Z= 0.329 Chirality : 0.043 0.156 1441 Planarity : 0.004 0.065 1628 Dihedral : 13.010 72.929 1456 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.98 % Allowed : 21.19 % Favored : 75.82 % 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: 0.83 (0.26), residues: 1113 helix: 1.57 (0.24), residues: 469 sheet: -0.17 (0.36), residues: 197 loop : -0.09 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 791 HIS 0.003 0.001 HIS E 535 PHE 0.016 0.001 PHE E 464 TYR 0.022 0.002 TYR E 449 ARG 0.007 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 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 TYR cc_start: 0.5763 (OUTLIER) cc_final: 0.5290 (t80) REVERT: E 310 MET cc_start: 0.7849 (ptm) cc_final: 0.7638 (ptm) REVERT: E 507 THR cc_start: 0.8795 (m) cc_final: 0.8503 (p) REVERT: E 621 LEU cc_start: 0.8576 (mt) cc_final: 0.8372 (mt) REVERT: E 812 MET cc_start: 0.8730 (ttm) cc_final: 0.8506 (ttt) REVERT: E 1126 TRP cc_start: 0.3332 (m-10) cc_final: 0.1884 (m-10) REVERT: E 1164 LEU cc_start: 0.7219 (pp) cc_final: 0.6606 (mt) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.2275 time to fit residues: 40.3025 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 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 544 ASP Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 587 GLU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 954 ILE Chi-restraints excluded: chain E residue 957 SER Chi-restraints excluded: chain E residue 1003 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.151721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.120743 restraints weight = 20495.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.123929 restraints weight = 10297.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125912 restraints weight = 6785.645| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9686 Z= 0.172 Angle : 0.613 11.020 13202 Z= 0.310 Chirality : 0.042 0.153 1441 Planarity : 0.004 0.067 1628 Dihedral : 12.943 74.828 1456 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.16 % Allowed : 21.60 % Favored : 76.23 % 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: 1.00 (0.26), residues: 1113 helix: 1.76 (0.24), residues: 470 sheet: -0.15 (0.37), residues: 197 loop : -0.04 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 841 HIS 0.003 0.001 HIS E 921 PHE 0.015 0.001 PHE E 464 TYR 0.025 0.001 TYR E 842 ARG 0.007 0.001 ARG E 968 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.49 seconds wall clock time: 38 minutes 7.70 seconds (2287.70 seconds total)