Starting phenix.real_space_refine on Thu Mar 6 07:52:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ns4_12560/03_2025/7ns4_12560.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ns4_12560/03_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_12560/03_2025/7ns4_12560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_2025/7ns4_12560.map" model { file = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_2025/7ns4_12560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ns4_12560/03_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-5624/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: 3.69, per 1000 atoms: 0.68 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: 1.24 Conformation dependent library (CDL) restraints added in 607.7 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: 0.53 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: 1.28 Time building geometry restraints manager: 1.49 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: 1.060 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.800 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- 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 5576 Z= 0.394 Angle : 0.795 9.870 7550 Z= 0.409 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 *********************** 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 : 0.785 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: 0.1983 time to fit residues: 19.7059 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 : 0.591 ------------------------------------------------------------------------------- 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: 0.6980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 32 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.120044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106184 restraints weight = 8935.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107801 restraints weight = 5951.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109050 restraints weight = 4487.324| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5576 Z= 0.163 Angle : 0.598 8.244 7550 Z= 0.305 Chirality : 0.040 0.180 888 Planarity : 0.004 0.039 936 Dihedral : 4.843 23.252 726 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.19 % Allowed : 7.99 % Favored : 90.82 % 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: -0.32 (0.35), residues: 674 helix: 1.03 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.51 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.004 0.000 ARG b 86 *********************** 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 : 0.638 Fit side-chains REVERT: b 11 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7449 (mt-10) REVERT: b 320 GLN cc_start: 0.8046 (tp40) cc_final: 0.7633 (tp40) REVERT: i 361 ASP cc_start: 0.7824 (t0) cc_final: 0.7443 (t0) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1830 time to fit residues: 20.3051 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 : 0.652 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.0020 chunk 38 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.117247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103245 restraints weight = 9176.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104840 restraints weight = 6224.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106041 restraints weight = 4731.312| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5576 Z= 0.243 Angle : 0.628 9.665 7550 Z= 0.319 Chirality : 0.041 0.186 888 Planarity : 0.004 0.038 936 Dihedral : 4.908 23.418 726 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.89 % Allowed : 11.05 % Favored : 86.05 % 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: -0.23 (0.35), residues: 674 helix: 1.12 (0.26), residues: 421 sheet: None (None), residues: 0 loop : -2.46 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP i 356 HIS 0.004 0.001 HIS b 356 PHE 0.013 0.002 PHE b 344 TYR 0.015 0.001 TYR i 95 ARG 0.004 0.000 ARG b 86 *********************** 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 84 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.634 Fit side-chains REVERT: b 319 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8619 (m-10) REVERT: b 320 GLN cc_start: 0.8244 (tp40) cc_final: 0.7831 (tp40) REVERT: i 68 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7496 (tm-30) REVERT: i 361 ASP cc_start: 0.7860 (t0) cc_final: 0.7451 (t0) outliers start: 17 outliers final: 9 residues processed: 81 average time/residue: 0.1551 time to fit residues: 17.1353 Evaluate side-chains 71 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 25 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102920 restraints weight = 9404.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104573 restraints weight = 6296.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105746 restraints weight = 4730.002| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5576 Z= 0.238 Angle : 0.632 9.555 7550 Z= 0.317 Chirality : 0.041 0.189 888 Planarity : 0.004 0.038 936 Dihedral : 4.867 22.956 726 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.38 % Allowed : 13.10 % Favored : 84.52 % 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: -0.24 (0.35), residues: 674 helix: 1.09 (0.26), residues: 427 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP i 356 HIS 0.003 0.001 HIS b 356 PHE 0.013 0.001 PHE b 344 TYR 0.015 0.001 TYR i 95 ARG 0.003 0.000 ARG i 79 *********************** 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 78 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.670 Fit side-chains REVERT: b 319 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8675 (m-10) REVERT: b 320 GLN cc_start: 0.8302 (tp40) cc_final: 0.7881 (tp40) REVERT: i 68 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7377 (tm-30) REVERT: i 361 ASP cc_start: 0.7879 (t0) cc_final: 0.7462 (t0) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.1653 time to fit residues: 16.8569 Evaluate side-chains 69 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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=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: 1.9990 chunk 19 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.117843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103798 restraints weight = 9174.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105473 restraints weight = 6160.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106568 restraints weight = 4640.791| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5576 Z= 0.215 Angle : 0.603 9.419 7550 Z= 0.306 Chirality : 0.040 0.187 888 Planarity : 0.003 0.038 936 Dihedral : 4.749 22.998 726 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.21 % Allowed : 15.14 % Favored : 82.65 % 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: -0.11 (0.35), residues: 674 helix: 1.22 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.49 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP i 356 HIS 0.004 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 b 86 *********************** 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 80 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.626 Fit side-chains REVERT: b 47 LEU cc_start: 0.9110 (tp) cc_final: 0.8826 (tt) REVERT: b 319 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8710 (m-10) REVERT: b 320 GLN cc_start: 0.8488 (tp40) cc_final: 0.8106 (tp40) REVERT: i 68 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7309 (tm-30) REVERT: i 361 ASP cc_start: 0.7893 (t0) cc_final: 0.7458 (t0) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.1496 time to fit residues: 15.7292 Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 8 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.117210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103274 restraints weight = 9243.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104880 restraints weight = 6233.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106154 restraints weight = 4697.677| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5576 Z= 0.246 Angle : 0.615 8.929 7550 Z= 0.314 Chirality : 0.041 0.189 888 Planarity : 0.004 0.038 936 Dihedral : 4.797 22.515 726 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.74 % Allowed : 16.16 % Favored : 80.10 % 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: -0.13 (0.35), residues: 674 helix: 1.21 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.53 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 356 HIS 0.004 0.001 HIS b 356 PHE 0.016 0.002 PHE i 7 TYR 0.015 0.001 TYR i 95 ARG 0.004 0.000 ARG i 79 *********************** 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 81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.584 Fit side-chains REVERT: b 319 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: b 320 GLN cc_start: 0.8515 (tp40) cc_final: 0.8135 (tp40) REVERT: i 68 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7232 (tm-30) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 0.1382 time to fit residues: 14.5989 Evaluate side-chains 72 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.4980 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.0060 chunk 27 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.121789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107888 restraints weight = 9046.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109482 restraints weight = 5977.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110767 restraints weight = 4556.181| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5576 Z= 0.147 Angle : 0.570 8.695 7550 Z= 0.288 Chirality : 0.038 0.181 888 Planarity : 0.003 0.039 936 Dihedral : 4.360 21.536 726 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.89 % Allowed : 18.37 % Favored : 78.74 % 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: 0.21 (0.35), residues: 674 helix: 1.50 (0.27), residues: 424 sheet: None (None), residues: 0 loop : -2.40 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP i 356 HIS 0.005 0.001 HIS b 354 PHE 0.011 0.001 PHE b 351 TYR 0.011 0.001 TYR i 185 ARG 0.003 0.000 ARG i 79 *********************** 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 92 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.596 Fit side-chains REVERT: b 11 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7508 (mt-10) REVERT: b 319 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8686 (m-10) REVERT: b 320 GLN cc_start: 0.8461 (tp40) cc_final: 0.8059 (tp40) REVERT: i 20 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: i 68 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7104 (tm-30) REVERT: i 361 ASP cc_start: 0.7876 (t0) cc_final: 0.7667 (t0) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.1434 time to fit residues: 17.0110 Evaluate side-chains 78 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 207 LEU 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: 0.0060 chunk 53 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.118535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104675 restraints weight = 9197.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106338 restraints weight = 6171.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107569 restraints weight = 4655.561| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5576 Z= 0.221 Angle : 0.618 8.817 7550 Z= 0.309 Chirality : 0.040 0.184 888 Planarity : 0.004 0.039 936 Dihedral : 4.547 21.372 726 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.23 % Allowed : 18.71 % 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 (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: 0.12 (0.35), residues: 674 helix: 1.40 (0.26), residues: 427 sheet: None (None), residues: 0 loop : -2.42 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.013 0.001 PHE b 344 TYR 0.014 0.001 TYR i 95 ARG 0.004 0.000 ARG i 79 *********************** 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 82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.686 Fit side-chains REVERT: b 151 MET cc_start: 0.8431 (ptp) cc_final: 0.8183 (ptm) REVERT: b 319 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8683 (m-10) REVERT: b 320 GLN cc_start: 0.8521 (tp40) cc_final: 0.8162 (tp40) REVERT: i 20 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: i 68 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7125 (tm-30) outliers start: 19 outliers final: 12 residues processed: 77 average time/residue: 0.1847 time to fit residues: 18.5780 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 : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 LYS 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 328 ILE Chi-restraints excluded: chain b residue 377 LEU 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 207 LEU Chi-restraints excluded: chain i residue 454 ILE 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 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.117792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103657 restraints weight = 9218.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105304 restraints weight = 6208.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106558 restraints weight = 4713.575| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5576 Z= 0.236 Angle : 0.633 8.840 7550 Z= 0.316 Chirality : 0.041 0.188 888 Planarity : 0.004 0.039 936 Dihedral : 4.645 21.567 726 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.06 % Allowed : 19.56 % Favored : 77.38 % 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: 1.38 (0.26), residues: 426 sheet: None (None), residues: 0 loop : -2.49 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP i 356 HIS 0.004 0.001 HIS b 354 PHE 0.013 0.001 PHE b 344 TYR 0.016 0.002 TYR i 95 ARG 0.004 0.000 ARG i 79 *********************** 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 78 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.603 Fit side-chains REVERT: b 151 MET cc_start: 0.8408 (ptp) cc_final: 0.8180 (ptm) REVERT: b 169 ILE cc_start: 0.7841 (tp) cc_final: 0.7630 (tt) REVERT: b 319 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8727 (m-10) REVERT: b 320 GLN cc_start: 0.8522 (tp40) cc_final: 0.8168 (tp40) REVERT: i 20 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: i 68 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7170 (tm-30) outliers start: 18 outliers final: 13 residues processed: 75 average time/residue: 0.1756 time to fit residues: 17.4564 Evaluate side-chains 75 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 LYS 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 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 207 LEU Chi-restraints excluded: chain i residue 454 ILE Chi-restraints excluded: chain i residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 62 optimal weight: 0.0270 chunk 52 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 64 optimal weight: 0.2980 chunk 57 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.1476 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.122518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108391 restraints weight = 9084.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110181 restraints weight = 5981.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111318 restraints weight = 4459.035| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5576 Z= 0.145 Angle : 0.580 8.683 7550 Z= 0.289 Chirality : 0.038 0.181 888 Planarity : 0.004 0.040 936 Dihedral : 4.265 20.579 726 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.21 % Allowed : 20.58 % Favored : 77.21 % 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 (0.35), residues: 674 helix: 1.65 (0.26), residues: 424 sheet: None (None), residues: 0 loop : -2.39 (0.42), 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 0.012 0.001 PHE b 351 TYR 0.016 0.001 TYR i 95 ARG 0.004 0.000 ARG i 79 ********************** 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 84 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.665 Fit side-chains REVERT: b 11 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7521 (mt-10) REVERT: b 151 MET cc_start: 0.8383 (ptp) cc_final: 0.8145 (ptm) REVERT: b 189 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8593 (tttt) REVERT: b 319 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8671 (m-10) REVERT: b 320 GLN cc_start: 0.8473 (tp40) cc_final: 0.8087 (tp40) REVERT: i 20 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8313 (pm20) REVERT: i 68 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7025 (tm-30) REVERT: i 382 TYR cc_start: 0.9300 (m-80) cc_final: 0.9013 (m-80) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.1839 time to fit residues: 19.0479 Evaluate side-chains 76 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 207 LEU 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: 0.0470 chunk 13 optimal weight: 0.0270 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.121785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107628 restraints weight = 9183.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109318 restraints weight = 6062.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110659 restraints weight = 4517.254| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5576 Z= 0.160 Angle : 0.588 8.365 7550 Z= 0.294 Chirality : 0.039 0.179 888 Planarity : 0.004 0.043 936 Dihedral : 4.240 20.256 726 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.21 % Allowed : 20.58 % Favored : 77.21 % 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: 0.47 (0.35), residues: 674 helix: 1.71 (0.26), residues: 425 sheet: None (None), residues: 0 loop : -2.31 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP i 356 HIS 0.002 0.001 HIS b 32 PHE 0.011 0.001 PHE b 351 TYR 0.015 0.001 TYR i 95 ARG 0.004 0.000 ARG i 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.03 seconds wall clock time: 32 minutes 20.04 seconds (1940.04 seconds total)