Starting phenix.real_space_refine on Thu Jul 24 06:13:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ns4_12560/07_2025/7ns4_12560.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ns4_12560/07_2025/7ns4_12560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ns4_12560/07_2025/7ns4_12560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ns4_12560/07_2025/7ns4_12560.map" model { file = "/net/cci-nas-00/data/ceres_data/7ns4_12560/07_2025/7ns4_12560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ns4_12560/07_2025/7ns4_12560.cif" } resolution = 3.9 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 25 5.16 5 C 3534 2.51 5 N 924 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5465 Number of models: 1 Model: "" Number of chains: 4 Chain: "b" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2649 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 5 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 88 Chain: "i" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2814 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 343} Chain breaks: 5 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2349 SG CYS b 379 57.902 85.341 19.708 1.00 52.55 S ATOM 2524 SG CYS b 401 54.671 86.716 21.660 1.00 47.36 S ATOM 2530 SG CYS b 404 58.085 87.851 22.564 1.00 70.82 S ATOM 4696 SG CYS i 395 49.363 58.083 32.758 1.00 31.89 S ATOM 4844 SG CYS i 434 52.288 56.532 35.017 1.00 21.26 S ATOM 4864 SG CYS i 437 51.293 54.917 31.840 1.00 20.06 S Time building chain proxies: 4.03, per 1000 atoms: 0.74 Number of scatterers: 5465 At special positions: 0 Unit cell: (97.96, 99.54, 129.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 25 16.00 O 980 8.00 N 924 7.00 C 3534 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: 1.47 Conformation dependent library (CDL) restraints added in 600.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 381 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 404 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 379 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 401 " pdb=" ZN i 601 " pdb="ZN ZN i 601 " - pdb=" NE2 HIS b 356 " pdb="ZN ZN i 601 " - pdb=" SG CYS i 434 " pdb="ZN ZN i 601 " - pdb=" SG CYS i 395 " pdb="ZN ZN i 601 " - pdb=" SG CYS i 437 " Number of angles added : 6 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 59.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'b' and resid 3 through 15 removed outlier: 3.697A pdb=" N GLU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS b 14 " --> pdb=" O THR b 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE b 15 " --> pdb=" O GLU b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 54 removed outlier: 4.353A pdb=" N CYS b 29 " --> pdb=" O ASN b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 113 removed outlier: 4.826A pdb=" N GLU b 79 " --> pdb=" O GLU b 75 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN b 107 " --> pdb=" O SER b 103 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS b 108 " --> pdb=" O ASN b 104 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER b 109 " --> pdb=" O ARG b 105 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN b 112 " --> pdb=" O LYS b 108 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS b 113 " --> pdb=" O SER b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 119 through 122 No H-bonds generated for 'chain 'b' and resid 119 through 122' Processing helix chain 'b' and resid 134 through 146 removed outlier: 3.632A pdb=" N GLY b 140 " --> pdb=" O ASN b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 166 removed outlier: 4.495A pdb=" N GLN b 161 " --> pdb=" O ASN b 157 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR b 162 " --> pdb=" O GLU b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 188 removed outlier: 4.679A pdb=" N GLU b 176 " --> pdb=" O LYS b 172 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE b 177 " --> pdb=" O GLU b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 201 removed outlier: 4.504A pdb=" N LYS b 197 " --> pdb=" O GLU b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 210 through 223 Processing helix chain 'b' and resid 285 through 300 removed outlier: 4.253A pdb=" N SER b 290 " --> pdb=" O LYS b 286 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU b 291 " --> pdb=" O GLU b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 329 removed outlier: 3.765A pdb=" N PHE b 319 " --> pdb=" O GLY b 315 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLN b 320 " --> pdb=" O LEU b 316 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE b 321 " --> pdb=" O ILE b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 354 Processing helix chain 'b' and resid 386 through 392 Processing helix chain 'i' and resid 12 through 19 removed outlier: 3.812A pdb=" N LEU i 16 " --> pdb=" O VAL i 12 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS i 17 " --> pdb=" O ASP i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 59 removed outlier: 3.835A pdb=" N LEU i 29 " --> pdb=" O ILE i 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG i 33 " --> pdb=" O LEU i 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE i 34 " --> pdb=" O LEU i 30 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA i 39 " --> pdb=" O LYS i 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE i 41 " --> pdb=" O THR i 37 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS i 46 " --> pdb=" O ASN i 42 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER i 47 " --> pdb=" O LYS i 43 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA i 54 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU i 55 " --> pdb=" O HIS i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 117 removed outlier: 4.237A pdb=" N ALA i 72 " --> pdb=" O GLU i 68 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE i 84 " --> pdb=" O LYS i 80 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN i 97 " --> pdb=" O LYS i 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG i 105 " --> pdb=" O ARG i 101 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE i 109 " --> pdb=" O ARG i 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU i 112 " --> pdb=" O PHE i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 153 removed outlier: 4.122A pdb=" N TRP i 138 " --> pdb=" O LYS i 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU i 146 " --> pdb=" O TYR i 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP i 149 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG i 153 " --> pdb=" O ASP i 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 169 through 177 Processing helix chain 'i' and resid 186 through 199 removed outlier: 3.957A pdb=" N LEU i 199 " --> pdb=" O SER i 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 213 removed outlier: 4.168A pdb=" N GLU i 213 " --> pdb=" O SER i 209 " (cutoff:3.500A) Processing helix chain 'i' and resid 215 through 221 removed outlier: 3.943A pdb=" N THR i 219 " --> pdb=" O LYS i 215 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS i 220 " --> pdb=" O LYS i 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS i 221 " --> pdb=" O THR i 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 215 through 221' Processing helix chain 'i' and resid 226 through 235 Processing helix chain 'i' and resid 354 through 371 Processing helix chain 'i' and resid 378 through 389 removed outlier: 4.253A pdb=" N SER i 388 " --> pdb=" O SER i 384 " (cutoff:3.500A) Processing helix chain 'i' and resid 421 through 428 Processing helix chain 'i' and resid 441 through 446 Processing helix chain 'i' and resid 474 through 485 Processing sheet with id=AA1, first strand: chain 'i' and resid 509 through 514 removed outlier: 3.924A pdb=" N MET i 513 " --> pdb=" O PRO i 462 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE i 463 " --> pdb=" O TYR i 471 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU i 465 " --> pdb=" O ASN i 469 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN i 469 " --> pdb=" O LEU i 465 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL b 416 " --> pdb=" O PRO b 374 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU b 377 " --> pdb=" O HIS b 381 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N HIS b 381 " --> pdb=" O LEU b 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'i' and resid 495 through 498 removed outlier: 3.549A pdb=" N LYS i 503 " --> pdb=" O ASP i 498 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1713 1.35 - 1.47: 1354 1.47 - 1.59: 2473 1.59 - 1.72: 0 1.72 - 1.84: 36 Bond restraints: 5576 Sorted by residual: bond pdb=" CG1 ILE b 311 " pdb=" CD1 ILE b 311 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" CB LEU i 146 " pdb=" CG LEU i 146 " ideal model delta sigma weight residual 1.530 1.506 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" CB THR i 392 " pdb=" CG2 THR i 392 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CA THR i 152 " pdb=" C THR i 152 " ideal model delta sigma weight residual 1.518 1.470 0.048 4.01e-02 6.22e+02 1.44e+00 bond pdb=" CG LEU i 385 " pdb=" CD1 LEU i 385 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 ... (remaining 5571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 7312 1.97 - 3.95: 197 3.95 - 5.92: 30 5.92 - 7.90: 7 7.90 - 9.87: 4 Bond angle restraints: 7550 Sorted by residual: angle pdb=" CA GLN b 85 " pdb=" CB GLN b 85 " pdb=" CG GLN b 85 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.76e+00 angle pdb=" C PRO b 343 " pdb=" N PHE b 344 " pdb=" CA PHE b 344 " ideal model delta sigma weight residual 123.91 128.99 -5.08 1.66e+00 3.63e-01 9.36e+00 angle pdb=" CG1 ILE i 454 " pdb=" CB ILE i 454 " pdb=" CG2 ILE i 454 " ideal model delta sigma weight residual 110.70 101.85 8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" CA PRO i 449 " pdb=" C PRO i 449 " pdb=" N PHE i 450 " ideal model delta sigma weight residual 114.75 118.95 -4.20 1.45e+00 4.76e-01 8.38e+00 angle pdb=" CA LEU i 205 " pdb=" CB LEU i 205 " pdb=" CG LEU i 205 " ideal model delta sigma weight residual 116.30 126.17 -9.87 3.50e+00 8.16e-02 7.95e+00 ... (remaining 7545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3010 17.43 - 34.85: 285 34.85 - 52.28: 54 52.28 - 69.70: 9 69.70 - 87.13: 4 Dihedral angle restraints: 3362 sinusoidal: 1285 harmonic: 2077 Sorted by residual: dihedral pdb=" CA PHE b 344 " pdb=" C PHE b 344 " pdb=" N ASP b 345 " pdb=" CA ASP b 345 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER i 374 " pdb=" C SER i 374 " pdb=" N GLN i 375 " pdb=" CA GLN i 375 " ideal model delta harmonic sigma weight residual 180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU b 21 " pdb=" C LEU b 21 " pdb=" N GLU b 22 " pdb=" CA GLU b 22 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 670 0.051 - 0.103: 185 0.103 - 0.154: 27 0.154 - 0.205: 3 0.205 - 0.256: 3 Chirality restraints: 888 Sorted by residual: chirality pdb=" CG LEU b 21 " pdb=" CB LEU b 21 " pdb=" CD1 LEU b 21 " pdb=" CD2 LEU b 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE b 344 " pdb=" N PHE b 344 " pdb=" C PHE b 344 " pdb=" CB PHE b 344 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE i 454 " pdb=" CA ILE i 454 " pdb=" CG1 ILE i 454 " pdb=" CG2 ILE i 454 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 885 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET b 151 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO b 152 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO b 152 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO b 152 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 302 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ILE b 302 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE b 302 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE b 303 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE i 25 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO i 26 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO i 26 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO i 26 " -0.020 5.00e-02 4.00e+02 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 95 2.67 - 3.23: 5503 3.23 - 3.79: 7874 3.79 - 4.34: 9977 4.34 - 4.90: 16438 Nonbonded interactions: 39887 Sorted by model distance: nonbonded pdb=" N SER b 2 " pdb=" OD1 ASP i 13 " model vdw 2.116 3.120 nonbonded pdb=" O PHE i 7 " pdb=" OD1 ASN i 8 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR i 471 " pdb=" OD1 ASP i 498 " model vdw 2.194 3.040 nonbonded pdb=" ND2 ASN i 467 " pdb=" OD2 ASP i 498 " model vdw 2.209 3.120 nonbonded pdb=" O LEU i 22 " pdb=" NH1 ARG i 105 " model vdw 2.212 3.120 ... (remaining 39882 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: 1.870 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.006 0.056 5584 Z= 0.255 Angle : 0.811 9.870 7556 Z= 0.411 Chirality : 0.048 0.256 888 Planarity : 0.004 0.051 936 Dihedral : 14.398 87.130 1994 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.34), residues: 674 helix: 0.47 (0.26), residues: 433 sheet: -2.03 (1.80), residues: 10 loop : -2.89 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP i 356 HIS 0.008 0.001 HIS b 356 PHE 0.017 0.002 PHE b 303 TYR 0.015 0.002 TYR i 95 ARG 0.006 0.001 ARG b 86 Details of bonding type rmsd hydrogen bonds : bond 0.06632 ( 273) hydrogen bonds : angle 4.64676 ( 819) metal coordination : bond 0.02203 ( 8) metal coordination : angle 5.84443 ( 6) covalent geometry : bond 0.00610 ( 5576) covalent geometry : angle 0.79490 ( 7550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.632 Fit side-chains REVERT: i 361 ASP cc_start: 0.7924 (t0) cc_final: 0.7649 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1911 time to fit residues: 19.1037 Evaluate side-chains 61 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.1980 chunk 52 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 32 optimal weight: 0.0470 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105602 restraints weight = 8997.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107267 restraints weight = 6061.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108397 restraints weight = 4564.546| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5584 Z= 0.121 Angle : 0.604 8.173 7556 Z= 0.308 Chirality : 0.040 0.181 888 Planarity : 0.004 0.040 936 Dihedral : 4.889 23.463 726 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 1.19 % Allowed : 7.65 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.34), residues: 674 helix: 1.01 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.53 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.015 0.001 PHE b 303 TYR 0.012 0.001 TYR i 185 ARG 0.003 0.000 ARG b 86 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 273) hydrogen bonds : angle 3.77165 ( 819) metal coordination : bond 0.01117 ( 8) metal coordination : angle 1.88800 ( 6) covalent geometry : bond 0.00252 ( 5576) covalent geometry : angle 0.60213 ( 7550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.673 Fit side-chains REVERT: b 11 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7442 (mt-10) REVERT: b 47 LEU cc_start: 0.9100 (tp) cc_final: 0.8865 (tt) REVERT: b 320 GLN cc_start: 0.8044 (tp40) cc_final: 0.7656 (tp40) REVERT: i 361 ASP cc_start: 0.7825 (t0) cc_final: 0.7447 (t0) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1701 time to fit residues: 19.0535 Evaluate side-chains 68 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101457 restraints weight = 9191.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103006 restraints weight = 6250.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104189 restraints weight = 4776.292| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5584 Z= 0.195 Angle : 0.672 9.778 7556 Z= 0.338 Chirality : 0.043 0.190 888 Planarity : 0.004 0.039 936 Dihedral : 5.100 23.511 726 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.06 % Allowed : 11.05 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.34), residues: 674 helix: 0.92 (0.26), residues: 426 sheet: -2.01 (1.79), residues: 10 loop : -2.58 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP i 356 HIS 0.004 0.001 HIS b 356 PHE 0.015 0.002 PHE b 344 TYR 0.015 0.002 TYR i 95 ARG 0.004 0.000 ARG b 86 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 273) hydrogen bonds : angle 3.96044 ( 819) metal coordination : bond 0.00711 ( 8) metal coordination : angle 2.82076 ( 6) covalent geometry : bond 0.00465 ( 5576) covalent geometry : angle 0.66716 ( 7550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.655 Fit side-chains REVERT: b 319 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8634 (m-10) REVERT: b 320 GLN cc_start: 0.8295 (tp40) cc_final: 0.7925 (tp40) REVERT: i 68 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7604 (tm-30) REVERT: i 361 ASP cc_start: 0.7878 (t0) cc_final: 0.7476 (t0) outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 0.1568 time to fit residues: 16.8056 Evaluate side-chains 73 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 205 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN i 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101262 restraints weight = 9425.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102882 restraints weight = 6334.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103947 restraints weight = 4797.267| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5584 Z= 0.189 Angle : 0.666 9.725 7556 Z= 0.333 Chirality : 0.042 0.192 888 Planarity : 0.004 0.038 936 Dihedral : 5.084 23.260 726 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.72 % Allowed : 14.97 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.34), residues: 674 helix: 0.90 (0.26), residues: 427 sheet: -2.07 (1.79), residues: 10 loop : -2.60 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP i 356 HIS 0.004 0.001 HIS b 356 PHE 0.014 0.002 PHE b 344 TYR 0.015 0.002 TYR i 95 ARG 0.005 0.000 ARG b 86 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 273) hydrogen bonds : angle 3.93608 ( 819) metal coordination : bond 0.00971 ( 8) metal coordination : angle 2.88607 ( 6) covalent geometry : bond 0.00448 ( 5576) covalent geometry : angle 0.66158 ( 7550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.721 Fit side-chains REVERT: b 319 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8595 (m-10) REVERT: b 320 GLN cc_start: 0.8508 (tp40) cc_final: 0.8153 (tp40) REVERT: i 68 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7480 (tm-30) REVERT: i 115 ILE cc_start: 0.8129 (mt) cc_final: 0.7914 (mt) REVERT: i 361 ASP cc_start: 0.7905 (t0) cc_final: 0.7485 (t0) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.1631 time to fit residues: 17.5576 Evaluate side-chains 75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain b residue 361 CYS Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 29 LEU Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 205 LEU Chi-restraints excluded: chain i residue 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101338 restraints weight = 9227.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102955 restraints weight = 6257.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104134 restraints weight = 4758.355| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5584 Z= 0.184 Angle : 0.660 9.911 7556 Z= 0.330 Chirality : 0.042 0.192 888 Planarity : 0.004 0.037 936 Dihedral : 5.052 23.361 726 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.89 % Allowed : 17.35 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.34), residues: 674 helix: 0.95 (0.26), residues: 427 sheet: None (None), residues: 0 loop : -2.56 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP i 356 HIS 0.006 0.001 HIS b 354 PHE 0.014 0.002 PHE b 344 TYR 0.014 0.001 TYR i 95 ARG 0.005 0.000 ARG b 86 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 273) hydrogen bonds : angle 3.90243 ( 819) metal coordination : bond 0.00975 ( 8) metal coordination : angle 2.81275 ( 6) covalent geometry : bond 0.00435 ( 5576) covalent geometry : angle 0.65553 ( 7550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.623 Fit side-chains REVERT: b 319 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: b 320 GLN cc_start: 0.8524 (tp40) cc_final: 0.8180 (tp40) REVERT: i 68 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7510 (tm-30) REVERT: i 361 ASP cc_start: 0.7912 (t0) cc_final: 0.7478 (t0) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1537 time to fit residues: 17.1252 Evaluate side-chains 76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 205 LEU Chi-restraints excluded: chain i residue 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 465 LEU Chi-restraints excluded: chain i residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 12 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 201 ASN i 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103269 restraints weight = 9210.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104925 restraints weight = 6209.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105990 restraints weight = 4705.929| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5584 Z= 0.152 Angle : 0.621 10.129 7556 Z= 0.313 Chirality : 0.041 0.189 888 Planarity : 0.004 0.038 936 Dihedral : 4.832 22.812 726 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.08 % Allowed : 18.20 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.35), residues: 674 helix: 1.10 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP i 356 HIS 0.003 0.001 HIS b 354 PHE 0.012 0.001 PHE b 344 TYR 0.014 0.001 TYR i 95 ARG 0.004 0.000 ARG i 79 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 273) hydrogen bonds : angle 3.77358 ( 819) metal coordination : bond 0.01096 ( 8) metal coordination : angle 2.45495 ( 6) covalent geometry : bond 0.00351 ( 5576) covalent geometry : angle 0.61732 ( 7550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.614 Fit side-chains REVERT: b 319 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8683 (m-10) REVERT: b 320 GLN cc_start: 0.8510 (tp40) cc_final: 0.8143 (tp40) REVERT: i 20 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: i 68 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7270 (tm-30) REVERT: i 146 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9161 (tt) REVERT: i 361 ASP cc_start: 0.7893 (t0) cc_final: 0.7441 (t0) outliers start: 24 outliers final: 13 residues processed: 84 average time/residue: 0.1586 time to fit residues: 18.1015 Evaluate side-chains 76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 361 CYS Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 397 ILE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 20 GLN Chi-restraints excluded: chain i residue 59 PHE Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 146 LEU Chi-restraints excluded: chain i residue 205 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 465 LEU Chi-restraints excluded: chain i residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.0040 chunk 27 optimal weight: 0.0040 chunk 60 optimal weight: 0.0270 overall best weight: 0.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 87 GLN i 8 ASN i 97 GLN ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110685 restraints weight = 9106.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112518 restraints weight = 5904.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113774 restraints weight = 4355.862| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5584 Z= 0.106 Angle : 0.554 9.114 7556 Z= 0.281 Chirality : 0.038 0.181 888 Planarity : 0.003 0.039 936 Dihedral : 4.216 20.782 726 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.23 % Allowed : 18.88 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.35), residues: 674 helix: 1.48 (0.27), residues: 422 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.011 0.001 PHE b 351 TYR 0.009 0.001 TYR i 185 ARG 0.003 0.000 ARG i 79 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 273) hydrogen bonds : angle 3.46074 ( 819) metal coordination : bond 0.01608 ( 8) metal coordination : angle 1.98752 ( 6) covalent geometry : bond 0.00215 ( 5576) covalent geometry : angle 0.55135 ( 7550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.608 Fit side-chains REVERT: b 319 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (m-10) REVERT: b 320 GLN cc_start: 0.8450 (tp40) cc_final: 0.8021 (tp40) REVERT: i 68 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7037 (tm-30) REVERT: i 382 TYR cc_start: 0.9304 (m-80) cc_final: 0.9016 (m-80) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 0.1407 time to fit residues: 18.3619 Evaluate side-chains 75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 397 ILE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 8 ASN Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 112 ASN i 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103226 restraints weight = 9292.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104871 restraints weight = 6208.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106067 restraints weight = 4691.058| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5584 Z= 0.190 Angle : 0.674 9.989 7556 Z= 0.337 Chirality : 0.042 0.188 888 Planarity : 0.004 0.038 936 Dihedral : 4.683 20.529 726 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.38 % Allowed : 20.58 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.35), residues: 674 helix: 1.26 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.51 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP i 356 HIS 0.004 0.001 HIS b 356 PHE 0.018 0.002 PHE i 7 TYR 0.013 0.002 TYR i 185 ARG 0.004 0.000 ARG i 79 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 273) hydrogen bonds : angle 3.81471 ( 819) metal coordination : bond 0.00614 ( 8) metal coordination : angle 2.39842 ( 6) covalent geometry : bond 0.00454 ( 5576) covalent geometry : angle 0.67112 ( 7550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.633 Fit side-chains REVERT: b 47 LEU cc_start: 0.9097 (tp) cc_final: 0.8810 (tt) REVERT: b 319 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8698 (m-10) REVERT: b 320 GLN cc_start: 0.8540 (tp40) cc_final: 0.8206 (tp40) REVERT: i 68 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7144 (tm-30) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.1547 time to fit residues: 14.3122 Evaluate side-chains 63 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 124 VAL Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 328 ILE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.2980 chunk 44 optimal weight: 0.0010 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 overall best weight: 0.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105972 restraints weight = 9164.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107721 restraints weight = 6082.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108813 restraints weight = 4544.126| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5584 Z= 0.128 Angle : 0.617 9.011 7556 Z= 0.307 Chirality : 0.040 0.185 888 Planarity : 0.004 0.040 936 Dihedral : 4.466 20.978 726 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.38 % Allowed : 20.92 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.35), residues: 674 helix: 1.41 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.50 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP i 356 HIS 0.003 0.001 HIS b 354 PHE 0.012 0.001 PHE b 351 TYR 0.011 0.001 TYR i 185 ARG 0.004 0.000 ARG i 79 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 273) hydrogen bonds : angle 3.61141 ( 819) metal coordination : bond 0.00905 ( 8) metal coordination : angle 1.73825 ( 6) covalent geometry : bond 0.00284 ( 5576) covalent geometry : angle 0.61498 ( 7550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: b 151 MET cc_start: 0.8475 (ptp) cc_final: 0.8243 (ptm) REVERT: b 169 ILE cc_start: 0.7726 (tp) cc_final: 0.7521 (tt) REVERT: b 189 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8611 (tttt) REVERT: b 319 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8708 (m-10) REVERT: b 320 GLN cc_start: 0.8492 (tp40) cc_final: 0.8118 (tp40) REVERT: i 20 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: i 68 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7082 (tm-30) outliers start: 14 outliers final: 9 residues processed: 76 average time/residue: 0.1943 time to fit residues: 19.2401 Evaluate side-chains 75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 199 CYS Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 319 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 397 ILE Chi-restraints excluded: chain i residue 20 GLN Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 0.0020 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 chunk 62 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 63 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 overall best weight: 0.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 8 ASN ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110739 restraints weight = 9155.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112588 restraints weight = 5917.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113769 restraints weight = 4352.307| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5584 Z= 0.108 Angle : 0.587 8.256 7556 Z= 0.292 Chirality : 0.038 0.176 888 Planarity : 0.004 0.041 936 Dihedral : 4.137 19.413 726 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.38 % Allowed : 21.43 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.35), residues: 674 helix: 1.61 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.35 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.013 0.001 PHE b 351 TYR 0.010 0.001 TYR i 185 ARG 0.005 0.000 ARG i 86 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 273) hydrogen bonds : angle 3.41950 ( 819) metal coordination : bond 0.01141 ( 8) metal coordination : angle 1.72827 ( 6) covalent geometry : bond 0.00225 ( 5576) covalent geometry : angle 0.58514 ( 7550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.658 Fit side-chains REVERT: b 151 MET cc_start: 0.8365 (ptp) cc_final: 0.8133 (ptm) REVERT: b 169 ILE cc_start: 0.7514 (tp) cc_final: 0.7296 (tt) REVERT: b 189 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8579 (tttt) REVERT: b 303 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: b 320 GLN cc_start: 0.8476 (tp40) cc_final: 0.8076 (tp40) REVERT: i 33 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7651 (mmt180) REVERT: i 508 SER cc_start: 0.8349 (m) cc_final: 0.8083 (p) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.1744 time to fit residues: 19.4668 Evaluate side-chains 78 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 199 CYS Chi-restraints excluded: chain b residue 302 ILE Chi-restraints excluded: chain b residue 303 PHE Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 397 ILE Chi-restraints excluded: chain i residue 7 PHE Chi-restraints excluded: chain i residue 8 ASN Chi-restraints excluded: chain i residue 107 GLU Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 454 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 8 ASN ** i 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111848 restraints weight = 9198.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112799 restraints weight = 6095.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113372 restraints weight = 4927.348| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 5584 Z= 0.185 Angle : 1.047 59.195 7556 Z= 0.625 Chirality : 0.046 0.704 888 Planarity : 0.005 0.083 936 Dihedral : 4.325 34.600 726 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.42 % Favored : 92.43 % Rotamer: Outliers : 2.04 % Allowed : 21.60 % Favored : 76.36 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.33 (0.35), residues: 674 helix: 1.61 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.37 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP i 356 HIS 0.003 0.001 HIS b 354 PHE 0.012 0.001 PHE b 351 TYR 0.020 0.001 TYR i 382 ARG 0.003 0.000 ARG i 79 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 273) hydrogen bonds : angle 3.42285 ( 819) metal coordination : bond 0.01037 ( 8) metal coordination : angle 1.75095 ( 6) covalent geometry : bond 0.00347 ( 5576) covalent geometry : angle 1.04659 ( 7550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.62 seconds wall clock time: 34 minutes 28.92 seconds (2068.92 seconds total)