Starting phenix.real_space_refine on Tue Mar 3 13:40:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ns4_12560/03_2026/7ns4_12560.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ns4_12560/03_2026/7ns4_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_2026/7ns4_12560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_2026/7ns4_12560.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_2026/7ns4_12560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_2026/7ns4_12560.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'ASP:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 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: {'GLU:plan': 12, 'GLN:plan1': 3, 'ASP:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} 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: 1.28, per 1000 atoms: 0.23 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: 0.42 Conformation dependent library (CDL) restraints added in 259.0 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: 0.12 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: 0.50 Time building geometry restraints manager: 0.54 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.490 Find NCS groups from input model: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.001 ARG b 86 TYR 0.015 0.002 TYR i 95 PHE 0.017 0.002 PHE b 303 TRP 0.020 0.002 TRP i 356 HIS 0.008 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 5576) covalent geometry : angle 0.79490 ( 7550) hydrogen bonds : bond 0.06632 ( 273) hydrogen bonds : angle 4.64676 ( 819) metal coordination : bond 0.02203 ( 8) metal coordination : angle 5.84443 ( 6) *********************** 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 : 0.205 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: 0.0759 time to fit residues: 7.6146 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101745 restraints weight = 9217.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103411 restraints weight = 6194.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104484 restraints weight = 4691.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105339 restraints weight = 3860.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105751 restraints weight = 3352.592| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5584 Z= 0.169 Angle : 0.659 8.646 7556 Z= 0.333 Chirality : 0.042 0.187 888 Planarity : 0.004 0.040 936 Dihedral : 5.230 23.982 726 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 1.36 % Allowed : 9.18 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.34), residues: 674 helix: 0.79 (0.26), residues: 426 sheet: -1.94 (1.80), residues: 10 loop : -2.72 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 79 TYR 0.015 0.002 TYR i 95 PHE 0.012 0.002 PHE b 351 TRP 0.012 0.002 TRP i 356 HIS 0.004 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5576) covalent geometry : angle 0.65487 ( 7550) hydrogen bonds : bond 0.05104 ( 273) hydrogen bonds : angle 4.04382 ( 819) metal coordination : bond 0.01008 ( 8) metal coordination : angle 2.72696 ( 6) *********************** 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 76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.150 Fit side-chains REVERT: i 361 ASP cc_start: 0.7887 (t0) cc_final: 0.7502 (t0) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.0702 time to fit residues: 7.0606 Evaluate side-chains 67 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 b residue 361 CYS 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 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 46 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.117809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103812 restraints weight = 9119.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105434 restraints weight = 6119.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106658 restraints weight = 4637.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107410 restraints weight = 3777.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107990 restraints weight = 3278.418| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5584 Z= 0.140 Angle : 0.603 9.970 7556 Z= 0.307 Chirality : 0.040 0.185 888 Planarity : 0.004 0.038 936 Dihedral : 4.900 23.832 726 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.38 % Allowed : 11.05 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.34), residues: 674 helix: 1.08 (0.27), residues: 419 sheet: None (None), residues: 0 loop : -2.49 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 79 TYR 0.013 0.001 TYR i 185 PHE 0.012 0.001 PHE b 351 TRP 0.008 0.001 TRP i 356 HIS 0.003 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5576) covalent geometry : angle 0.60017 ( 7550) hydrogen bonds : bond 0.04653 ( 273) hydrogen bonds : angle 3.81914 ( 819) metal coordination : bond 0.00891 ( 8) metal coordination : angle 2.27495 ( 6) *********************** 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 82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: b 319 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8686 (m-10) REVERT: i 361 ASP cc_start: 0.7825 (t0) cc_final: 0.7403 (t0) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.0721 time to fit residues: 7.5495 Evaluate side-chains 67 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 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 7 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 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 = 0.3276 r_free = 0.3276 target = 0.115137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101034 restraints weight = 9259.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102636 restraints weight = 6293.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103817 restraints weight = 4770.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104566 restraints weight = 3913.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105157 restraints weight = 3407.706| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1060 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 : 0.663 9.662 7556 Z= 0.335 Chirality : 0.043 0.191 888 Planarity : 0.004 0.045 936 Dihedral : 5.103 23.516 726 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.89 % Allowed : 15.14 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.34), residues: 674 helix: 0.88 (0.26), residues: 427 sheet: -2.15 (1.76), residues: 10 loop : -2.61 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 86 TYR 0.014 0.002 TYR i 95 PHE 0.014 0.002 PHE b 344 TRP 0.021 0.002 TRP i 356 HIS 0.004 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 5576) covalent geometry : angle 0.65851 ( 7550) hydrogen bonds : bond 0.05162 ( 273) hydrogen bonds : angle 3.95504 ( 819) metal coordination : bond 0.00902 ( 8) metal coordination : angle 2.88567 ( 6) *********************** 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 79 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.238 Fit side-chains REVERT: b 319 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8621 (m-10) REVERT: i 361 ASP cc_start: 0.7896 (t0) cc_final: 0.7468 (t0) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.0785 time to fit residues: 7.8835 Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain i residue 489 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 46 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 65 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.118115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103928 restraints weight = 9278.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105608 restraints weight = 6161.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106860 restraints weight = 4625.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107575 restraints weight = 3767.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108195 restraints weight = 3279.615| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5584 Z= 0.135 Angle : 0.595 9.771 7556 Z= 0.302 Chirality : 0.040 0.186 888 Planarity : 0.004 0.038 936 Dihedral : 4.767 23.068 726 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.55 % Allowed : 16.50 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.35), residues: 674 helix: 1.16 (0.26), residues: 421 sheet: None (None), residues: 0 loop : -2.45 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 79 TYR 0.012 0.001 TYR i 95 PHE 0.011 0.001 PHE b 351 TRP 0.013 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5576) covalent geometry : angle 0.59165 ( 7550) hydrogen bonds : bond 0.04504 ( 273) hydrogen bonds : angle 3.70983 ( 819) metal coordination : bond 0.01012 ( 8) metal coordination : angle 2.16348 ( 6) *********************** 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: 15 poor density : 70 time to evaluate : 0.148 Fit side-chains REVERT: b 319 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8683 (m-10) REVERT: i 68 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7261 (tm-30) REVERT: i 361 ASP cc_start: 0.7864 (t0) cc_final: 0.7419 (t0) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.0696 time to fit residues: 7.5262 Evaluate side-chains 74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 53 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 87 GLN b 201 ASN i 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102584 restraints weight = 9215.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104216 restraints weight = 6224.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105375 restraints weight = 4709.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105871 restraints weight = 3859.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105880 restraints weight = 3451.495| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5584 Z= 0.168 Angle : 0.631 9.093 7556 Z= 0.319 Chirality : 0.041 0.189 888 Planarity : 0.004 0.039 936 Dihedral : 4.863 22.736 726 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.42 % Allowed : 17.01 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.35), residues: 674 helix: 1.04 (0.26), residues: 427 sheet: None (None), residues: 0 loop : -2.56 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 79 TYR 0.014 0.001 TYR i 95 PHE 0.013 0.001 PHE b 344 TRP 0.011 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5576) covalent geometry : angle 0.62633 ( 7550) hydrogen bonds : bond 0.04821 ( 273) hydrogen bonds : angle 3.80645 ( 819) metal coordination : bond 0.00899 ( 8) metal coordination : angle 2.64722 ( 6) *********************** 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 85 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.206 Fit side-chains REVERT: b 319 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: b 320 GLN cc_start: 0.8443 (tp40) cc_final: 0.8177 (tp-100) REVERT: i 68 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7359 (tm-30) outliers start: 26 outliers final: 15 residues processed: 77 average time/residue: 0.0626 time to fit residues: 6.6733 Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 151 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.0060 chunk 58 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4374 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103090 restraints weight = 9271.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104755 restraints weight = 6233.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105933 restraints weight = 4715.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106770 restraints weight = 3876.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107322 restraints weight = 3333.319| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1445 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= 0.160 Angle : 0.637 9.683 7556 Z= 0.319 Chirality : 0.041 0.189 888 Planarity : 0.004 0.038 936 Dihedral : 4.807 22.581 726 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.91 % Allowed : 18.03 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.35), residues: 674 helix: 1.09 (0.26), residues: 425 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 79 TYR 0.013 0.001 TYR i 95 PHE 0.013 0.001 PHE b 344 TRP 0.011 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5576) covalent geometry : angle 0.63312 ( 7550) hydrogen bonds : bond 0.04676 ( 273) hydrogen bonds : angle 3.77786 ( 819) metal coordination : bond 0.00970 ( 8) metal coordination : angle 2.48214 ( 6) *********************** 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 83 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.226 Fit side-chains REVERT: b 319 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8688 (m-10) REVERT: i 20 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: i 68 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7311 (tm-30) outliers start: 23 outliers final: 17 residues processed: 76 average time/residue: 0.0623 time to fit residues: 6.6097 Evaluate side-chains 77 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 124 VAL 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 328 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100324 restraints weight = 9333.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101858 restraints weight = 6416.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103074 restraints weight = 4897.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103759 restraints weight = 4028.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104336 restraints weight = 3534.291| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5584 Z= 0.220 Angle : 0.701 9.339 7556 Z= 0.352 Chirality : 0.043 0.195 888 Planarity : 0.004 0.041 936 Dihedral : 5.109 22.880 726 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.74 % Allowed : 18.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.34), residues: 674 helix: 0.88 (0.26), residues: 426 sheet: -2.33 (1.77), residues: 10 loop : -2.69 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 79 TYR 0.015 0.002 TYR i 185 PHE 0.016 0.002 PHE b 344 TRP 0.008 0.001 TRP i 356 HIS 0.004 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 5576) covalent geometry : angle 0.69566 ( 7550) hydrogen bonds : bond 0.05321 ( 273) hydrogen bonds : angle 4.00754 ( 819) metal coordination : bond 0.00959 ( 8) metal coordination : angle 3.15990 ( 6) *********************** 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 80 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.224 Fit side-chains REVERT: b 87 GLN cc_start: 0.7929 (mm110) cc_final: 0.7500 (tp40) REVERT: b 319 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8618 (m-10) REVERT: i 20 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: i 68 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7453 (tm-30) outliers start: 22 outliers final: 16 residues processed: 75 average time/residue: 0.0608 time to fit residues: 6.3171 Evaluate side-chains 74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 119 ILE Chi-restraints excluded: chain b residue 124 VAL 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 328 ILE Chi-restraints excluded: chain b residue 377 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 50 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 320 GLN i 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107682 restraints weight = 9133.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109170 restraints weight = 6304.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110314 restraints weight = 4850.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110974 restraints weight = 4018.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111500 restraints weight = 3522.931| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5584 Z= 0.116 Angle : 0.599 10.798 7556 Z= 0.298 Chirality : 0.039 0.186 888 Planarity : 0.004 0.040 936 Dihedral : 4.468 21.508 726 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.23 % Allowed : 19.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.35), residues: 674 helix: 1.28 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.49 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 79 TYR 0.011 0.001 TYR i 185 PHE 0.010 0.001 PHE b 351 TRP 0.014 0.001 TRP i 356 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5576) covalent geometry : angle 0.59678 ( 7550) hydrogen bonds : bond 0.03971 ( 273) hydrogen bonds : angle 3.57224 ( 819) metal coordination : bond 0.01461 ( 8) metal coordination : angle 1.97029 ( 6) *********************** 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 90 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.173 Fit side-chains REVERT: b 160 PHE cc_start: 0.7580 (t80) cc_final: 0.7169 (t80) REVERT: b 169 ILE cc_start: 0.7995 (tp) cc_final: 0.7792 (tt) REVERT: b 319 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: i 20 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: i 68 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7136 (tm-30) REVERT: i 382 TYR cc_start: 0.9304 (m-80) cc_final: 0.9014 (m-80) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 0.0524 time to fit residues: 6.1258 Evaluate side-chains 74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU 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 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 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 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105099 restraints weight = 9248.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106815 restraints weight = 6144.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108067 restraints weight = 4606.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108784 restraints weight = 3745.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109361 restraints weight = 3243.563| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5584 Z= 0.136 Angle : 0.624 10.262 7556 Z= 0.310 Chirality : 0.040 0.184 888 Planarity : 0.004 0.043 936 Dihedral : 4.534 21.089 726 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.55 % Allowed : 20.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.35), residues: 674 helix: 1.30 (0.26), residues: 427 sheet: None (None), residues: 0 loop : -2.45 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 79 TYR 0.013 0.001 TYR i 185 PHE 0.011 0.001 PHE b 344 TRP 0.033 0.002 TRP i 356 HIS 0.003 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5576) covalent geometry : angle 0.62145 ( 7550) hydrogen bonds : bond 0.04285 ( 273) hydrogen bonds : angle 3.62946 ( 819) metal coordination : bond 0.00839 ( 8) metal coordination : angle 2.15601 ( 6) ********************** 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 74 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.213 Fit side-chains REVERT: b 319 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8670 (m-10) REVERT: i 20 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: i 68 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7163 (tm-30) REVERT: i 382 TYR cc_start: 0.9271 (m-80) cc_final: 0.8989 (m-80) REVERT: i 471 TYR cc_start: 0.6518 (m-80) cc_final: 0.6252 (m-80) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.0608 time to fit residues: 5.8522 Evaluate side-chains 69 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU 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 377 LEU Chi-restraints excluded: chain b residue 397 ILE 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 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 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 67 optimal weight: 0.4980 chunk 2 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.0070 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 320 GLN i 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105793 restraints weight = 9264.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107563 restraints weight = 6109.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108785 restraints weight = 4569.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109601 restraints weight = 3713.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110256 restraints weight = 3192.962| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5584 Z= 0.129 Angle : 0.618 9.901 7556 Z= 0.306 Chirality : 0.040 0.184 888 Planarity : 0.004 0.043 936 Dihedral : 4.477 21.008 726 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.38 % Allowed : 20.75 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.35), residues: 674 helix: 1.34 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.45 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 79 TYR 0.013 0.001 TYR i 95 PHE 0.011 0.001 PHE b 351 TRP 0.029 0.002 TRP i 356 HIS 0.003 0.001 HIS b 356 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5576) covalent geometry : angle 0.61560 ( 7550) hydrogen bonds : bond 0.04191 ( 273) hydrogen bonds : angle 3.61119 ( 819) metal coordination : bond 0.01074 ( 8) metal coordination : angle 1.99305 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 904.00 seconds wall clock time: 16 minutes 18.64 seconds (978.64 seconds total)