Starting phenix.real_space_refine on Wed Feb 12 14:13:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukf_26579/02_2025/7ukf_26579.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukf_26579/02_2025/7ukf_26579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ukf_26579/02_2025/7ukf_26579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukf_26579/02_2025/7ukf_26579.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukf_26579/02_2025/7ukf_26579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukf_26579/02_2025/7ukf_26579.cif" } resolution = 3.02 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= 0.005 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 K 4 8.98 5 S 60 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8005 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' HG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1842 SG CYS A 406 56.243 52.488 57.734 1.00 69.40 S Restraints were copied for chains: B, C, D Time building chain proxies: 4.63, per 1000 atoms: 0.58 Number of scatterers: 8005 At special positions: 0 Unit cell: (113.162, 112.336, 84.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 K 4 19.00 S 60 16.00 O 1356 8.00 N 1332 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.602A pdb=" N SER A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 347 removed outlier: 5.088A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 206 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 293 removed outlier: 4.021A pdb=" N VAL B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL C 290 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.973A pdb=" N PHE C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL D 290 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1767 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: 2.06 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2440 1.34 - 1.46: 1907 1.46 - 1.58: 3757 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8196 Sorted by residual: bond pdb=" C VAL B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.17e-02 7.31e+03 1.22e+00 bond pdb=" C VAL A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" C VAL C 377 " pdb=" N PRO C 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" C VAL D 377 " pdb=" N PRO D 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.38e-01 ... (remaining 8191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 10563 1.22 - 2.45: 451 2.45 - 3.67: 90 3.67 - 4.89: 20 4.89 - 6.12: 12 Bond angle restraints: 11136 Sorted by residual: angle pdb=" N LEU C 400 " pdb=" CA LEU C 400 " pdb=" C LEU C 400 " ideal model delta sigma weight residual 109.81 115.30 -5.49 2.21e+00 2.05e-01 6.17e+00 angle pdb=" N LEU D 400 " pdb=" CA LEU D 400 " pdb=" C LEU D 400 " ideal model delta sigma weight residual 109.81 115.27 -5.46 2.21e+00 2.05e-01 6.11e+00 angle pdb=" N LEU A 400 " pdb=" CA LEU A 400 " pdb=" C LEU A 400 " ideal model delta sigma weight residual 109.81 115.26 -5.45 2.21e+00 2.05e-01 6.07e+00 angle pdb=" N LEU B 400 " pdb=" CA LEU B 400 " pdb=" C LEU B 400 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU C 271 " pdb=" C LEU C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 118.44 121.56 -3.12 1.59e+00 3.96e-01 3.85e+00 ... (remaining 11131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.14: 4010 10.14 - 20.28: 530 20.28 - 30.43: 176 30.43 - 40.57: 76 40.57 - 50.71: 12 Dihedral angle restraints: 4804 sinusoidal: 1772 harmonic: 3032 Sorted by residual: dihedral pdb=" CB MET D 333 " pdb=" CG MET D 333 " pdb=" SD MET D 333 " pdb=" CE MET D 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.71 -50.71 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET A 333 " pdb=" CG MET A 333 " pdb=" SD MET A 333 " pdb=" CE MET A 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.68 -50.68 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET B 333 " pdb=" CG MET B 333 " pdb=" SD MET B 333 " pdb=" CE MET B 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.66 -50.66 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 629 0.026 - 0.051: 416 0.051 - 0.077: 183 0.077 - 0.102: 71 0.102 - 0.128: 17 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CA VAL B 207 " pdb=" N VAL B 207 " pdb=" C VAL B 207 " pdb=" CB VAL B 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA VAL C 207 " pdb=" N VAL C 207 " pdb=" C VAL C 207 " pdb=" CB VAL C 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1313 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 357 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO C 358 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO D 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO B 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.025 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 2973 2.86 - 3.43: 9594 3.43 - 4.00: 14762 4.00 - 4.57: 21588 4.57 - 5.14: 30209 Nonbonded interactions: 79126 Sorted by model distance: nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR D 166 " pdb=" OE1 GLN D 169 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 166 " pdb=" OE1 GLN C 169 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR D 188 " pdb=" O PHE D 303 " model vdw 2.339 3.040 ... (remaining 79121 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 8.250 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.860 Find NCS groups from input model: 0.300 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.004 0.031 8196 Z= 0.261 Angle : 0.611 6.115 11136 Z= 0.349 Chirality : 0.041 0.128 1316 Planarity : 0.005 0.045 1364 Dihedral : 11.495 50.711 2852 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.20 (0.27), residues: 1028 helix: 0.91 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.83 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS C 414 PHE 0.010 0.001 PHE C 326 TYR 0.017 0.002 TYR C 188 ARG 0.002 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.838 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2280 time to fit residues: 37.3747 Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.211537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151807 restraints weight = 5692.587| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.69 r_work: 0.3288 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8196 Z= 0.413 Angle : 0.626 6.446 11136 Z= 0.329 Chirality : 0.044 0.139 1316 Planarity : 0.005 0.047 1364 Dihedral : 3.982 13.602 1148 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.47 % Allowed : 6.25 % Favored : 93.28 % 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: 0.60 (0.26), residues: 1028 helix: 0.65 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.24 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 172 HIS 0.003 0.001 HIS A 306 PHE 0.011 0.002 PHE D 326 TYR 0.021 0.002 TYR A 225 ARG 0.002 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.949 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 105 average time/residue: 0.2136 time to fit residues: 30.6236 Evaluate side-chains 102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.214813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155477 restraints weight = 6191.818| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.79 r_work: 0.3324 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8196 Z= 0.194 Angle : 0.518 5.975 11136 Z= 0.269 Chirality : 0.038 0.132 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.655 12.797 1148 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.12 % Allowed : 9.08 % Favored : 90.80 % 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: 1.17 (0.26), residues: 1028 helix: 1.04 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.07 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.002 0.000 HIS B 306 PHE 0.011 0.001 PHE D 326 TYR 0.018 0.001 TYR A 188 ARG 0.003 0.000 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.789 Fit side-chains REVERT: A 257 PHE cc_start: 0.6566 (t80) cc_final: 0.6284 (t80) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.1730 time to fit residues: 28.4924 Evaluate side-chains 106 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 98 optimal weight: 0.0060 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.214002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155535 restraints weight = 6493.501| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.59 r_work: 0.3435 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8196 Z= 0.235 Angle : 0.532 5.846 11136 Z= 0.279 Chirality : 0.039 0.132 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.611 12.695 1148 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.59 % Allowed : 11.56 % Favored : 87.85 % 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: 1.36 (0.26), residues: 1028 helix: 1.18 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.05 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.002 0.000 HIS A 306 PHE 0.011 0.001 PHE D 326 TYR 0.020 0.002 TYR C 273 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.870 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 119 average time/residue: 0.1658 time to fit residues: 28.5311 Evaluate side-chains 114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.214683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154401 restraints weight = 6741.308| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.87 r_work: 0.3576 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8196 Z= 0.219 Angle : 0.519 5.562 11136 Z= 0.272 Chirality : 0.039 0.133 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.534 12.261 1148 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 11.79 % Favored : 87.26 % 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: 1.56 (0.26), residues: 1028 helix: 1.34 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS B 306 PHE 0.011 0.001 PHE D 326 TYR 0.016 0.002 TYR A 188 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.942 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 121 average time/residue: 0.1776 time to fit residues: 31.3727 Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.213654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166005 restraints weight = 6753.179| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.05 r_work: 0.3495 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8196 Z= 0.261 Angle : 0.538 5.423 11136 Z= 0.282 Chirality : 0.040 0.131 1316 Planarity : 0.005 0.044 1364 Dihedral : 3.564 12.217 1148 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.18 % Allowed : 12.03 % Favored : 86.79 % 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: 1.58 (0.26), residues: 1028 helix: 1.34 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.02 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 172 HIS 0.002 0.001 HIS B 306 PHE 0.012 0.002 PHE D 257 TYR 0.015 0.002 TYR A 188 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.883 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 115 average time/residue: 0.1712 time to fit residues: 28.6292 Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.214526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167858 restraints weight = 6875.151| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.06 r_work: 0.3512 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8196 Z= 0.221 Angle : 0.518 5.162 11136 Z= 0.271 Chirality : 0.039 0.133 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.510 12.145 1148 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 13.56 % Favored : 85.26 % 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: 1.72 (0.26), residues: 1028 helix: 1.44 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.08 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 172 HIS 0.002 0.000 HIS B 306 PHE 0.013 0.001 PHE A 257 TYR 0.016 0.001 TYR A 188 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.911 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 124 average time/residue: 0.1856 time to fit residues: 32.1443 Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.214807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163846 restraints weight = 6952.981| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.32 r_work: 0.3295 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8196 Z= 0.212 Angle : 0.516 5.258 11136 Z= 0.270 Chirality : 0.039 0.132 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.482 12.144 1148 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.18 % Allowed : 13.56 % Favored : 85.26 % 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: 1.80 (0.26), residues: 1028 helix: 1.49 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.08 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 172 HIS 0.002 0.000 HIS B 306 PHE 0.015 0.001 PHE D 257 TYR 0.023 0.002 TYR A 273 ARG 0.003 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.847 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 124 average time/residue: 0.1670 time to fit residues: 29.9972 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.214029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167580 restraints weight = 6939.544| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.13 r_work: 0.3457 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8196 Z= 0.248 Angle : 0.537 5.374 11136 Z= 0.281 Chirality : 0.040 0.131 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.512 12.214 1148 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.18 % Allowed : 14.50 % Favored : 84.32 % 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: 1.74 (0.26), residues: 1028 helix: 1.46 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.04 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 172 HIS 0.002 0.001 HIS B 306 PHE 0.016 0.001 PHE D 257 TYR 0.022 0.002 TYR D 273 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.883 Fit side-chains REVERT: D 301 PHE cc_start: 0.8016 (m-80) cc_final: 0.7588 (m-10) outliers start: 10 outliers final: 10 residues processed: 124 average time/residue: 0.1868 time to fit residues: 32.4289 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4360 r_free = 0.4360 target = 0.215246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151176 restraints weight = 6886.755| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.75 r_work: 0.3350 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8196 Z= 0.203 Angle : 0.517 5.167 11136 Z= 0.269 Chirality : 0.038 0.133 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.456 12.130 1148 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 14.15 % Favored : 84.91 % 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: 1.87 (0.26), residues: 1028 helix: 1.55 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.04 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS B 306 PHE 0.017 0.001 PHE A 257 TYR 0.024 0.002 TYR B 273 ARG 0.002 0.000 ARG D 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.830 Fit side-chains REVERT: B 301 PHE cc_start: 0.7786 (m-80) cc_final: 0.7348 (m-10) REVERT: C 301 PHE cc_start: 0.7736 (m-80) cc_final: 0.7308 (m-10) REVERT: D 301 PHE cc_start: 0.7768 (m-80) cc_final: 0.7337 (m-10) outliers start: 8 outliers final: 8 residues processed: 123 average time/residue: 0.1668 time to fit residues: 29.5854 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.214197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166018 restraints weight = 6876.914| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.04 r_work: 0.3302 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8196 Z= 0.243 Angle : 0.534 5.189 11136 Z= 0.279 Chirality : 0.039 0.132 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.476 12.257 1148 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.18 % Allowed : 14.27 % Favored : 84.55 % 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: 2.28 (0.26), residues: 1028 helix: 1.88 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.38 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 362 HIS 0.002 0.000 HIS A 306 PHE 0.017 0.001 PHE D 257 TYR 0.021 0.002 TYR B 273 ARG 0.002 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.53 seconds wall clock time: 83 minutes 8.29 seconds (4988.29 seconds total)