Starting phenix.real_space_refine on Tue Mar 11 22:23:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t53_41042/03_2025/8t53_41042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t53_41042/03_2025/8t53_41042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t53_41042/03_2025/8t53_41042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t53_41042/03_2025/8t53_41042.map" model { file = "/net/cci-nas-00/data/ceres_data/8t53_41042/03_2025/8t53_41042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t53_41042/03_2025/8t53_41042.cif" } resolution = 4.1 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= 0.023 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4418 2.51 5 N 1094 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6660 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3330 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 5 Chain: "B" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3330 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 5 Time building chain proxies: 4.52, per 1000 atoms: 0.68 Number of scatterers: 6660 At special positions: 0 Unit cell: (98.8, 113.1, 91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1110 8.00 N 1094 7.00 C 4418 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: 1.60 Conformation dependent library (CDL) restraints added in 912.0 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 68.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 41 removed outlier: 3.812A pdb=" N LEU A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 72 removed outlier: 3.772A pdb=" N LEU A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP A 53 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 142 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.593A pdb=" N ASN A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.582A pdb=" N THR A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 307 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.625A pdb=" N ASN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.844A pdb=" N GLU A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP A 413 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.312A pdb=" N ALA A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.819A pdb=" N VAL A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'B' and resid 9 through 41 removed outlier: 3.821A pdb=" N LEU B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 4.270A pdb=" N THR B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 142 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 168 through 171 removed outlier: 4.070A pdb=" N MET B 171 " --> pdb=" O GLU B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 196 through 203 removed outlier: 4.308A pdb=" N ILE B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.569A pdb=" N THR B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 307 Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.632A pdb=" N ASN B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 413 removed outlier: 3.789A pdb=" N GLU B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 413 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.321A pdb=" N ALA B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.794A pdb=" N VAL B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 454 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 5.839A pdb=" N LYS A 147 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 176 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR A 149 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 178 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 151 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS A 148 " --> pdb=" O HIS A 210 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE A 212 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 150 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 320 Processing sheet with id=AA3, first strand: chain 'A' and resid 396 through 398 removed outlier: 6.285A pdb=" N LEU A 397 " --> pdb=" O THR A 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 179 removed outlier: 7.821A pdb=" N ILE B 151 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 178 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 148 " --> pdb=" O HIS B 210 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 212 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 150 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AA6, first strand: chain 'B' and resid 314 through 320 Processing sheet with id=AA7, first strand: chain 'B' and resid 396 through 398 removed outlier: 6.480A pdb=" N LEU B 397 " --> pdb=" O THR B 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 382 hydrogen bonds defined for protein. 1095 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: 1.81 Time building geometry restraints manager: 1.91 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: 1993 1.34 - 1.46: 1641 1.46 - 1.58: 3154 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6848 Sorted by residual: bond pdb=" CG GLN B 166 " pdb=" CD GLN B 166 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.64e-01 bond pdb=" CG PRO A 328 " pdb=" CD PRO A 328 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.94e-01 bond pdb=" CB PRO A 328 " pdb=" CG PRO A 328 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.11e-01 bond pdb=" C SER A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.83e-01 bond pdb=" C MET B 190 " pdb=" N LEU B 191 " ideal model delta sigma weight residual 1.331 1.343 -0.011 1.59e-02 3.96e+03 5.13e-01 ... (remaining 6843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9105 1.78 - 3.57: 141 3.57 - 5.35: 24 5.35 - 7.13: 6 7.13 - 8.91: 2 Bond angle restraints: 9278 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.42 108.43 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA PRO A 328 " pdb=" N PRO A 328 " pdb=" CD PRO A 328 " ideal model delta sigma weight residual 112.00 107.21 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.39 108.57 4.82 1.47e+00 4.63e-01 1.07e+01 angle pdb=" N PRO A 328 " pdb=" CD PRO A 328 " pdb=" CG PRO A 328 " ideal model delta sigma weight residual 103.20 98.55 4.65 1.50e+00 4.44e-01 9.60e+00 angle pdb=" CA TRP A 121 " pdb=" CB TRP A 121 " pdb=" CG TRP A 121 " ideal model delta sigma weight residual 113.60 107.89 5.71 1.90e+00 2.77e-01 9.02e+00 ... (remaining 9273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 3578 16.00 - 32.01: 338 32.01 - 48.01: 47 48.01 - 64.01: 5 64.01 - 80.01: 6 Dihedral angle restraints: 3974 sinusoidal: 1622 harmonic: 2352 Sorted by residual: dihedral pdb=" CA TRP A 121 " pdb=" C TRP A 121 " pdb=" N THR A 122 " pdb=" CA THR A 122 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLN B 44 " pdb=" C GLN B 44 " pdb=" N ARG B 45 " pdb=" CA ARG B 45 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN A 44 " pdb=" C GLN A 44 " pdb=" N ARG A 45 " pdb=" CA ARG A 45 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 769 0.042 - 0.084: 186 0.084 - 0.126: 64 0.126 - 0.168: 3 0.168 - 0.210: 2 Chirality restraints: 1024 Sorted by residual: chirality pdb=" CA TRP A 121 " pdb=" N TRP A 121 " pdb=" C TRP A 121 " pdb=" CB TRP A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA TRP B 121 " pdb=" N TRP B 121 " pdb=" C TRP B 121 " pdb=" CB TRP B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CG LEU B 125 " pdb=" CB LEU B 125 " pdb=" CD1 LEU B 125 " pdb=" CD2 LEU B 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1021 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 327 " -0.058 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 328 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 121 " 0.026 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 121 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 121 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 121 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 121 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 201 " 0.021 2.00e-02 2.50e+03 1.60e-02 6.36e+00 pdb=" CG TRP B 201 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 201 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 201 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 201 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 201 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 201 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 201 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 201 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 201 " -0.001 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 513 2.74 - 3.28: 7038 3.28 - 3.82: 11549 3.82 - 4.36: 12982 4.36 - 4.90: 21407 Nonbonded interactions: 53489 Sorted by model distance: nonbonded pdb=" O PHE A 60 " pdb=" OG SER A 63 " model vdw 2.201 3.040 nonbonded pdb=" O GLN A 51 " pdb=" OG1 THR A 54 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 164 " pdb=" OG SER A 167 " model vdw 2.210 3.040 nonbonded pdb=" O GLN B 51 " pdb=" OG1 THR B 54 " model vdw 2.220 3.040 nonbonded pdb=" O PHE B 60 " pdb=" OG SER B 63 " model vdw 2.221 3.040 ... (remaining 53484 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 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 : 0.002 0.042 6848 Z= 0.155 Angle : 0.590 8.914 9278 Z= 0.330 Chirality : 0.041 0.210 1024 Planarity : 0.005 0.085 1122 Dihedral : 12.603 80.013 2446 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.31), residues: 772 helix: 0.93 (0.24), residues: 464 sheet: -0.83 (0.59), residues: 86 loop : 0.61 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 121 HIS 0.003 0.001 HIS B 137 PHE 0.023 0.002 PHE A 91 TYR 0.011 0.001 TYR B 77 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7600 (pp20) cc_final: 0.7191 (pp20) REVERT: B 171 MET cc_start: 0.5928 (ptp) cc_final: 0.5650 (ptp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1726 time to fit residues: 23.6577 Evaluate side-chains 81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.250148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.217016 restraints weight = 23694.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.218056 restraints weight = 19133.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.220157 restraints weight = 15535.945| |-----------------------------------------------------------------------------| r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4989 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 6848 Z= 0.408 Angle : 0.794 6.910 9278 Z= 0.431 Chirality : 0.048 0.208 1024 Planarity : 0.006 0.058 1122 Dihedral : 5.774 26.126 872 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.41 % Allowed : 7.87 % Favored : 91.71 % 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 (0.30), residues: 772 helix: 0.51 (0.23), residues: 456 sheet: -0.65 (0.62), residues: 66 loop : 0.30 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 121 HIS 0.008 0.002 HIS B 137 PHE 0.030 0.003 PHE A 332 TYR 0.021 0.002 TYR B 115 ARG 0.005 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.746 Fit side-chains REVERT: A 92 ARG cc_start: 0.4940 (tpt170) cc_final: 0.4636 (mmt-90) REVERT: A 425 MET cc_start: -0.0496 (mtp) cc_final: -0.0781 (mtp) REVERT: B 73 ARG cc_start: 0.2454 (tpt170) cc_final: 0.2114 (tpt170) REVERT: B 263 MET cc_start: -0.0558 (mmp) cc_final: -0.1052 (mmp) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.1801 time to fit residues: 24.9851 Evaluate side-chains 83 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.260925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.227334 restraints weight = 22992.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.228653 restraints weight = 18473.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.230894 restraints weight = 15176.525| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4749 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6848 Z= 0.195 Angle : 0.589 6.761 9278 Z= 0.317 Chirality : 0.043 0.168 1024 Planarity : 0.005 0.055 1122 Dihedral : 4.965 22.995 872 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 0.78 (0.30), residues: 772 helix: 0.84 (0.23), residues: 474 sheet: -0.53 (0.62), residues: 66 loop : 0.48 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 121 HIS 0.012 0.001 HIS A 76 PHE 0.031 0.002 PHE A 60 TYR 0.021 0.002 TYR B 115 ARG 0.004 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.712 Fit side-chains REVERT: A 79 TYR cc_start: 0.8178 (t80) cc_final: 0.7889 (t80) REVERT: A 92 ARG cc_start: 0.4625 (tpt170) cc_final: 0.4362 (mmt-90) REVERT: A 180 ASP cc_start: 0.4773 (t70) cc_final: 0.4497 (t0) REVERT: A 201 TRP cc_start: 0.6404 (m100) cc_final: 0.5156 (m100) REVERT: B 40 PHE cc_start: 0.4546 (m-80) cc_final: 0.4242 (m-80) REVERT: B 73 ARG cc_start: 0.2621 (tpt170) cc_final: 0.2204 (tpt170) REVERT: B 121 TRP cc_start: 0.6743 (m-90) cc_final: 0.6343 (m-90) REVERT: B 190 MET cc_start: 0.6857 (ttt) cc_final: 0.6635 (ttt) REVERT: B 263 MET cc_start: -0.0026 (mmp) cc_final: -0.1177 (mmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1792 time to fit residues: 25.2115 Evaluate side-chains 85 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.5061 r_free = 0.5061 target = 0.260696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.225180 restraints weight = 23910.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.226443 restraints weight = 18910.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.228893 restraints weight = 15224.036| |-----------------------------------------------------------------------------| r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4819 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6848 Z= 0.186 Angle : 0.552 6.383 9278 Z= 0.299 Chirality : 0.042 0.157 1024 Planarity : 0.004 0.051 1122 Dihedral : 4.673 20.974 872 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 1.11 (0.31), residues: 772 helix: 1.08 (0.23), residues: 474 sheet: -0.41 (0.63), residues: 66 loop : 0.68 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 121 HIS 0.008 0.001 HIS A 76 PHE 0.019 0.001 PHE B 332 TYR 0.018 0.001 TYR A 162 ARG 0.008 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6591 (ttp-170) cc_final: 0.6228 (ttp-170) REVERT: A 79 TYR cc_start: 0.8162 (t80) cc_final: 0.7865 (t80) REVERT: A 92 ARG cc_start: 0.4897 (tpt170) cc_final: 0.4520 (mmt-90) REVERT: A 180 ASP cc_start: 0.4906 (t70) cc_final: 0.4673 (t0) REVERT: A 201 TRP cc_start: 0.6378 (m100) cc_final: 0.5216 (m100) REVERT: A 425 MET cc_start: -0.0604 (mtp) cc_final: -0.0805 (mtp) REVERT: B 73 ARG cc_start: 0.2803 (tpt170) cc_final: 0.2390 (tpt170) REVERT: B 79 TYR cc_start: 0.8167 (t80) cc_final: 0.7950 (t80) REVERT: B 121 TRP cc_start: 0.6589 (m-90) cc_final: 0.6177 (m-90) REVERT: B 263 MET cc_start: -0.0187 (mmp) cc_final: -0.1373 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1913 time to fit residues: 27.0382 Evaluate side-chains 87 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 0.0020 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 0.0010 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.263641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.229521 restraints weight = 24046.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.231161 restraints weight = 19467.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.232642 restraints weight = 15892.969| |-----------------------------------------------------------------------------| r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4745 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6848 Z= 0.144 Angle : 0.513 6.043 9278 Z= 0.278 Chirality : 0.041 0.170 1024 Planarity : 0.004 0.048 1122 Dihedral : 4.371 18.538 872 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 1.43 (0.31), residues: 772 helix: 1.36 (0.23), residues: 470 sheet: -0.24 (0.68), residues: 62 loop : 0.71 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 121 HIS 0.006 0.001 HIS A 76 PHE 0.010 0.001 PHE B 332 TYR 0.022 0.001 TYR A 77 ARG 0.006 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6386 (ttp-170) cc_final: 0.6086 (ttp-170) REVERT: A 79 TYR cc_start: 0.8070 (t80) cc_final: 0.7663 (t80) REVERT: A 92 ARG cc_start: 0.5031 (tpt170) cc_final: 0.4536 (mmt-90) REVERT: A 180 ASP cc_start: 0.4843 (t70) cc_final: 0.4630 (t0) REVERT: B 73 ARG cc_start: 0.3049 (tpt170) cc_final: 0.2650 (tpt170) REVERT: B 121 TRP cc_start: 0.6726 (m-90) cc_final: 0.6311 (m-90) REVERT: B 263 MET cc_start: -0.0078 (mmp) cc_final: -0.1218 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1893 time to fit residues: 27.4498 Evaluate side-chains 92 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 = 0.5057 r_free = 0.5057 target = 0.261620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.226180 restraints weight = 23472.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.228080 restraints weight = 19317.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.230572 restraints weight = 15586.689| |-----------------------------------------------------------------------------| r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4783 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6848 Z= 0.161 Angle : 0.533 6.043 9278 Z= 0.286 Chirality : 0.042 0.263 1024 Planarity : 0.004 0.043 1122 Dihedral : 4.395 18.688 872 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.31), residues: 772 helix: 1.34 (0.23), residues: 472 sheet: -0.02 (0.67), residues: 66 loop : 0.69 (0.47), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 121 HIS 0.005 0.001 HIS A 76 PHE 0.020 0.001 PHE A 91 TYR 0.013 0.001 TYR B 115 ARG 0.006 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.707 Fit side-chains REVERT: A 45 ARG cc_start: 0.6745 (ttp-170) cc_final: 0.6339 (ttp-170) REVERT: A 79 TYR cc_start: 0.8091 (t80) cc_final: 0.7721 (t80) REVERT: A 92 ARG cc_start: 0.4794 (tpt170) cc_final: 0.4462 (mmt-90) REVERT: A 180 ASP cc_start: 0.4806 (t70) cc_final: 0.4579 (t0) REVERT: A 201 TRP cc_start: 0.6378 (m100) cc_final: 0.5149 (m100) REVERT: B 73 ARG cc_start: 0.2550 (tpt170) cc_final: 0.2214 (tpt170) REVERT: B 121 TRP cc_start: 0.6825 (m-90) cc_final: 0.6398 (m-90) REVERT: B 263 MET cc_start: -0.0206 (mmp) cc_final: -0.1352 (mmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1776 time to fit residues: 24.8198 Evaluate side-chains 90 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.0470 chunk 57 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 overall best weight: 0.4686 ------------------------------------------------------------------------------- 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 = 0.5089 r_free = 0.5089 target = 0.264869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.237966 restraints weight = 22004.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.238895 restraints weight = 17471.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.239909 restraints weight = 14833.983| |-----------------------------------------------------------------------------| r_work (final): 0.4888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4503 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6848 Z= 0.145 Angle : 0.516 6.828 9278 Z= 0.276 Chirality : 0.041 0.169 1024 Planarity : 0.004 0.042 1122 Dihedral : 4.319 18.022 872 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 1.69 (0.31), residues: 772 helix: 1.53 (0.23), residues: 470 sheet: 0.17 (0.68), residues: 66 loop : 0.81 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 121 HIS 0.005 0.001 HIS A 76 PHE 0.018 0.001 PHE A 91 TYR 0.021 0.001 TYR B 77 ARG 0.005 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6699 (ttp-170) cc_final: 0.6422 (ttp-170) REVERT: A 79 TYR cc_start: 0.7918 (t80) cc_final: 0.7381 (t80) REVERT: A 92 ARG cc_start: 0.4971 (tpt170) cc_final: 0.4442 (mmt-90) REVERT: A 147 LYS cc_start: 0.6970 (pttt) cc_final: 0.6574 (pttt) REVERT: A 201 TRP cc_start: 0.6306 (m100) cc_final: 0.5112 (m100) REVERT: B 73 ARG cc_start: 0.3374 (tpt170) cc_final: 0.3016 (tpt170) REVERT: B 79 TYR cc_start: 0.7586 (t80) cc_final: 0.7200 (t80) REVERT: B 121 TRP cc_start: 0.6728 (m-90) cc_final: 0.6241 (m-90) REVERT: B 263 MET cc_start: -0.0315 (mmp) cc_final: -0.1372 (mmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1884 time to fit residues: 25.9711 Evaluate side-chains 90 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 = 0.5046 r_free = 0.5046 target = 0.258496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.219762 restraints weight = 23498.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.222657 restraints weight = 18520.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.225279 restraints weight = 15682.213| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6848 Z= 0.193 Angle : 0.570 6.280 9278 Z= 0.307 Chirality : 0.043 0.178 1024 Planarity : 0.004 0.043 1122 Dihedral : 4.658 19.220 872 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 1.38 (0.31), residues: 772 helix: 1.31 (0.23), residues: 472 sheet: -0.02 (0.67), residues: 66 loop : 0.65 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 121 HIS 0.003 0.001 HIS A 76 PHE 0.019 0.002 PHE A 91 TYR 0.015 0.001 TYR A 115 ARG 0.006 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.755 Fit side-chains REVERT: A 45 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6912 (ttp-170) REVERT: A 79 TYR cc_start: 0.8108 (t80) cc_final: 0.7855 (t80) REVERT: A 92 ARG cc_start: 0.4777 (tpt170) cc_final: 0.4424 (mmt-90) REVERT: A 142 LEU cc_start: 0.7818 (mt) cc_final: 0.7603 (mt) REVERT: A 144 ILE cc_start: 0.7601 (pt) cc_final: 0.7399 (pt) REVERT: A 147 LYS cc_start: 0.6960 (pttt) cc_final: 0.6721 (pttt) REVERT: A 201 TRP cc_start: 0.6397 (m100) cc_final: 0.5434 (m100) REVERT: B 73 ARG cc_start: 0.2582 (tpt170) cc_final: 0.2255 (tpt170) REVERT: B 79 TYR cc_start: 0.8085 (t80) cc_final: 0.7861 (t80) REVERT: B 121 TRP cc_start: 0.6730 (m-90) cc_final: 0.6142 (m-90) REVERT: B 201 TRP cc_start: 0.6065 (m100) cc_final: 0.4923 (m100) REVERT: B 263 MET cc_start: -0.0191 (mmp) cc_final: -0.1309 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1712 time to fit residues: 25.4655 Evaluate side-chains 98 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.5063 r_free = 0.5063 target = 0.261581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.227688 restraints weight = 22410.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.229507 restraints weight = 18023.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.232035 restraints weight = 14427.999| |-----------------------------------------------------------------------------| r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4774 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6848 Z= 0.161 Angle : 0.554 6.378 9278 Z= 0.295 Chirality : 0.042 0.169 1024 Planarity : 0.004 0.040 1122 Dihedral : 4.548 18.637 872 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.45 (0.31), residues: 772 helix: 1.34 (0.23), residues: 470 sheet: 0.06 (0.67), residues: 66 loop : 0.71 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 121 HIS 0.003 0.001 HIS A 76 PHE 0.020 0.001 PHE A 91 TYR 0.025 0.001 TYR B 77 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8128 (t80) cc_final: 0.7818 (t80) REVERT: A 92 ARG cc_start: 0.4827 (tpt170) cc_final: 0.4443 (mmt-90) REVERT: A 147 LYS cc_start: 0.6758 (pttt) cc_final: 0.6553 (pttt) REVERT: A 190 MET cc_start: 0.6968 (ttt) cc_final: 0.6727 (ttt) REVERT: B 73 ARG cc_start: 0.2846 (tpt170) cc_final: 0.2509 (tpt170) REVERT: B 121 TRP cc_start: 0.6679 (m-90) cc_final: 0.6074 (m-90) REVERT: B 150 ILE cc_start: 0.5814 (mm) cc_final: 0.5599 (mm) REVERT: B 263 MET cc_start: -0.0227 (mmp) cc_final: -0.1360 (mmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1856 time to fit residues: 27.1769 Evaluate side-chains 95 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 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 = 0.5323 r_free = 0.5323 target = 0.312394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.302469 restraints weight = 31141.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.303494 restraints weight = 21014.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.304241 restraints weight = 15638.602| |-----------------------------------------------------------------------------| r_work (final): 0.4987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4250 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6848 Z= 0.174 Angle : 0.577 6.458 9278 Z= 0.307 Chirality : 0.042 0.168 1024 Planarity : 0.004 0.044 1122 Dihedral : 4.574 18.654 872 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 1.39 (0.31), residues: 772 helix: 1.31 (0.23), residues: 472 sheet: -0.02 (0.66), residues: 66 loop : 0.66 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 121 HIS 0.003 0.001 HIS A 76 PHE 0.018 0.001 PHE A 46 TYR 0.015 0.001 TYR A 115 ARG 0.007 0.000 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8374 (mp10) cc_final: 0.7787 (mt0) REVERT: A 40 PHE cc_start: 0.3675 (m-80) cc_final: 0.3275 (m-80) REVERT: A 79 TYR cc_start: 0.7260 (t80) cc_final: 0.6590 (t80) REVERT: A 92 ARG cc_start: 0.5346 (tpt170) cc_final: 0.4509 (mmt-90) REVERT: A 190 MET cc_start: 0.7617 (ttt) cc_final: 0.7335 (ttt) REVERT: B 73 ARG cc_start: 0.4155 (tpt170) cc_final: 0.3817 (tpt170) REVERT: B 121 TRP cc_start: 0.6260 (m-90) cc_final: 0.5671 (m-90) REVERT: B 263 MET cc_start: -0.0354 (mmp) cc_final: -0.1521 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1820 time to fit residues: 26.9556 Evaluate side-chains 92 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.251423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.218050 restraints weight = 24109.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.219372 restraints weight = 19132.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.221295 restraints weight = 15414.379| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 6848 Z= 0.330 Angle : 0.761 9.455 9278 Z= 0.410 Chirality : 0.049 0.184 1024 Planarity : 0.005 0.043 1122 Dihedral : 5.631 24.311 872 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 0.38 (0.30), residues: 772 helix: 0.55 (0.23), residues: 466 sheet: -1.28 (0.61), residues: 68 loop : 0.48 (0.46), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 121 HIS 0.005 0.001 HIS A 234 PHE 0.042 0.003 PHE A 46 TYR 0.023 0.002 TYR B 8 ARG 0.006 0.001 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.60 seconds wall clock time: 50 minutes 20.37 seconds (3020.37 seconds total)