Starting phenix.real_space_refine on Tue Feb 11 22:46:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t53_41042/02_2025/8t53_41042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t53_41042/02_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_41042/02_2025/8t53_41042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t53_41042/02_2025/8t53_41042.map" model { file = "/net/cci-nas-00/data/ceres_data/8t53_41042/02_2025/8t53_41042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t53_41042/02_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-5592/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: 1.59 Conformation dependent library (CDL) restraints added in 853.4 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: 0.73 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: 1.97 Time building geometry restraints manager: 1.86 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: 0.940 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.960 Find NCS groups from input model: 0.230 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- 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 : 0.690 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: 0.1731 time to fit residues: 23.6630 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 : 0.748 ------------------------------------------------------------------------------- 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 = 0.217009 restraints weight = 23694.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.218008 restraints weight = 19135.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.219982 restraints weight = 15589.626| |-----------------------------------------------------------------------------| r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 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 : 0.729 Fit side-chains REVERT: A 92 ARG cc_start: 0.4963 (tpt170) cc_final: 0.4644 (mmt-90) REVERT: A 425 MET cc_start: -0.0491 (mtp) cc_final: -0.0785 (mtp) REVERT: B 73 ARG cc_start: 0.2441 (tpt170) cc_final: 0.2099 (tpt170) REVERT: B 263 MET cc_start: -0.0500 (mmp) cc_final: -0.0993 (mmp) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.1761 time to fit residues: 24.6091 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 : 0.681 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.5080 r_free = 0.5080 target = 0.261013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.226946 restraints weight = 23309.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.228634 restraints weight = 18721.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.230897 restraints weight = 15275.405| |-----------------------------------------------------------------------------| r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6848 Z= 0.185 Angle : 0.582 7.067 9278 Z= 0.313 Chirality : 0.043 0.167 1024 Planarity : 0.005 0.054 1122 Dihedral : 4.919 22.735 872 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 0.83 (0.30), residues: 772 helix: 0.88 (0.23), residues: 474 sheet: -0.50 (0.62), residues: 66 loop : 0.51 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 121 HIS 0.013 0.001 HIS A 76 PHE 0.031 0.002 PHE A 60 TYR 0.019 0.002 TYR A 162 ARG 0.018 0.001 ARG A 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 : 0.718 Fit side-chains REVERT: A 79 TYR cc_start: 0.8187 (t80) cc_final: 0.7923 (t80) REVERT: A 92 ARG cc_start: 0.4607 (tpt170) cc_final: 0.4369 (mmt-90) REVERT: A 180 ASP cc_start: 0.4753 (t70) cc_final: 0.4444 (t0) REVERT: A 201 TRP cc_start: 0.6536 (m100) cc_final: 0.5268 (m100) REVERT: B 40 PHE cc_start: 0.4617 (m-80) cc_final: 0.4304 (m-80) REVERT: B 73 ARG cc_start: 0.2553 (tpt170) cc_final: 0.2116 (tpt170) REVERT: B 121 TRP cc_start: 0.6748 (m-90) cc_final: 0.6318 (m-90) REVERT: B 190 MET cc_start: 0.6808 (ttt) cc_final: 0.6582 (ttt) REVERT: B 263 MET cc_start: -0.0011 (mmp) cc_final: -0.1151 (mmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1898 time to fit residues: 26.4100 Evaluate side-chains 82 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.5013 r_free = 0.5013 target = 0.253869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.219187 restraints weight = 23781.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.221078 restraints weight = 18321.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.223344 restraints weight = 14631.130| |-----------------------------------------------------------------------------| r_work (final): 0.4793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4935 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 6848 Z= 0.272 Angle : 0.646 6.363 9278 Z= 0.352 Chirality : 0.045 0.245 1024 Planarity : 0.005 0.067 1122 Dihedral : 5.233 24.093 872 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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: 0.68 (0.30), residues: 772 helix: 0.79 (0.23), residues: 470 sheet: -0.71 (0.60), residues: 66 loop : 0.40 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 121 HIS 0.007 0.001 HIS A 76 PHE 0.023 0.002 PHE B 332 TYR 0.020 0.002 TYR B 115 ARG 0.015 0.001 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 112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7118 (ttp-170) cc_final: 0.6310 (ttp80) REVERT: A 79 TYR cc_start: 0.8075 (t80) cc_final: 0.7762 (t80) REVERT: A 92 ARG cc_start: 0.4849 (tpt170) cc_final: 0.4503 (mmt-90) REVERT: A 180 ASP cc_start: 0.5554 (t70) cc_final: 0.5176 (t0) REVERT: A 201 TRP cc_start: 0.6594 (m100) cc_final: 0.5574 (m100) REVERT: A 263 MET cc_start: 0.0133 (mmp) cc_final: -0.0119 (mmp) REVERT: B 73 ARG cc_start: 0.2935 (tpt170) cc_final: 0.2521 (tpt170) REVERT: B 79 TYR cc_start: 0.8140 (t80) cc_final: 0.7866 (t80) REVERT: B 121 TRP cc_start: 0.6662 (m-90) cc_final: 0.6255 (m-90) REVERT: B 201 TRP cc_start: 0.6667 (m100) cc_final: 0.5462 (m100) REVERT: B 263 MET cc_start: 0.0150 (mmp) cc_final: -0.0070 (mmp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1866 time to fit residues: 27.9983 Evaluate side-chains 91 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- 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 = 0.5062 r_free = 0.5062 target = 0.260136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.225951 restraints weight = 23151.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.227251 restraints weight = 19167.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.229508 restraints weight = 15672.258| |-----------------------------------------------------------------------------| r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4767 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6848 Z= 0.170 Angle : 0.557 6.055 9278 Z= 0.301 Chirality : 0.043 0.262 1024 Planarity : 0.004 0.052 1122 Dihedral : 4.731 21.660 872 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.97 (0.31), residues: 772 helix: 1.02 (0.23), residues: 472 sheet: -0.56 (0.65), residues: 62 loop : 0.49 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 121 HIS 0.006 0.001 HIS A 76 PHE 0.024 0.001 PHE A 107 TYR 0.017 0.002 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 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7200 (ttp-170) cc_final: 0.6811 (ttp-170) REVERT: A 79 TYR cc_start: 0.8171 (t80) cc_final: 0.7883 (t80) REVERT: A 92 ARG cc_start: 0.4806 (tpt170) cc_final: 0.4431 (mmt-90) REVERT: A 180 ASP cc_start: 0.5262 (t70) cc_final: 0.4937 (t0) REVERT: B 73 ARG cc_start: 0.2739 (tpt170) cc_final: 0.2346 (tpt170) REVERT: B 79 TYR cc_start: 0.8032 (t80) cc_final: 0.7792 (t80) REVERT: B 121 TRP cc_start: 0.6846 (m-90) cc_final: 0.6239 (m-90) REVERT: B 263 MET cc_start: 0.0013 (mmp) cc_final: -0.1166 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1773 time to fit residues: 27.0330 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 : 0.667 ------------------------------------------------------------------------------- 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: 0.0980 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.5070 r_free = 0.5070 target = 0.263144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.228440 restraints weight = 23513.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.229620 restraints weight = 19285.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.231767 restraints weight = 16073.935| |-----------------------------------------------------------------------------| r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4762 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6848 Z= 0.140 Angle : 0.519 6.143 9278 Z= 0.279 Chirality : 0.041 0.170 1024 Planarity : 0.004 0.045 1122 Dihedral : 4.383 18.682 872 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.42 (0.31), residues: 772 helix: 1.36 (0.23), residues: 470 sheet: -0.17 (0.69), residues: 62 loop : 0.65 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 121 HIS 0.006 0.001 HIS A 76 PHE 0.010 0.001 PHE B 332 TYR 0.013 0.001 TYR B 8 ARG 0.007 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 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.6953 (ttp-170) cc_final: 0.6615 (ttp-170) REVERT: A 79 TYR cc_start: 0.8144 (t80) cc_final: 0.7836 (t80) REVERT: A 92 ARG cc_start: 0.4811 (tpt170) cc_final: 0.4452 (mmt-90) REVERT: B 73 ARG cc_start: 0.2735 (tpt170) cc_final: 0.2358 (tpt170) REVERT: B 121 TRP cc_start: 0.6773 (m-90) cc_final: 0.6282 (m-90) REVERT: B 216 GLU cc_start: 0.4110 (mp0) cc_final: 0.3886 (mp0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1886 time to fit residues: 27.5045 Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 0.0030 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.261548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.230377 restraints weight = 23381.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.230134 restraints weight = 20426.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.231836 restraints weight = 17896.072| |-----------------------------------------------------------------------------| r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4692 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6848 Z= 0.151 Angle : 0.528 6.382 9278 Z= 0.282 Chirality : 0.041 0.169 1024 Planarity : 0.004 0.045 1122 Dihedral : 4.374 17.974 872 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 1.48 (0.31), residues: 772 helix: 1.42 (0.23), residues: 470 sheet: -0.11 (0.70), residues: 62 loop : 0.65 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 121 HIS 0.004 0.001 HIS A 76 PHE 0.012 0.001 PHE B 332 TYR 0.023 0.001 TYR B 77 ARG 0.004 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 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7138 (ttp-170) cc_final: 0.6731 (ttp-170) REVERT: A 79 TYR cc_start: 0.8094 (t80) cc_final: 0.7805 (t80) REVERT: A 92 ARG cc_start: 0.4949 (tpt170) cc_final: 0.4588 (mmt-90) REVERT: A 147 LYS cc_start: 0.6603 (pttt) cc_final: 0.6327 (pttt) REVERT: A 201 TRP cc_start: 0.6487 (m100) cc_final: 0.5131 (m100) REVERT: B 73 ARG cc_start: 0.2743 (tpt170) cc_final: 0.2405 (tpt170) REVERT: B 121 TRP cc_start: 0.6987 (m-90) cc_final: 0.6344 (m-90) REVERT: B 147 LYS cc_start: 0.5874 (pttt) cc_final: 0.5655 (pttt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1951 time to fit residues: 28.3262 Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 0.9990 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 56 optimal weight: 0.0010 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.5045 r_free = 0.5045 target = 0.258840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.226538 restraints weight = 23841.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.226359 restraints weight = 20938.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.228105 restraints weight = 17906.249| |-----------------------------------------------------------------------------| r_work (final): 0.4816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4767 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6848 Z= 0.171 Angle : 0.574 8.050 9278 Z= 0.304 Chirality : 0.042 0.168 1024 Planarity : 0.004 0.048 1122 Dihedral : 4.614 19.875 872 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 1.30 (0.31), residues: 772 helix: 1.27 (0.23), residues: 472 sheet: -0.15 (0.71), residues: 62 loop : 0.57 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 121 HIS 0.004 0.001 HIS A 76 PHE 0.014 0.001 PHE B 332 TYR 0.016 0.001 TYR B 8 ARG 0.007 0.000 ARG A 80 *********************** 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 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6808 (ttp-170) REVERT: A 79 TYR cc_start: 0.8154 (t80) cc_final: 0.7810 (t80) REVERT: A 92 ARG cc_start: 0.4686 (tpt170) cc_final: 0.4470 (mmt-90) REVERT: A 147 LYS cc_start: 0.6662 (pttt) cc_final: 0.6445 (pttt) REVERT: A 190 MET cc_start: 0.7397 (ttt) cc_final: 0.7188 (ttt) REVERT: B 73 ARG cc_start: 0.2668 (tpt170) cc_final: 0.2321 (tpt170) REVERT: B 121 TRP cc_start: 0.6973 (m-90) cc_final: 0.6367 (m-90) REVERT: B 147 LYS cc_start: 0.5771 (pttt) cc_final: 0.5562 (pttt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1723 time to fit residues: 25.8442 Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.5044 r_free = 0.5044 target = 0.258182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.225419 restraints weight = 23690.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.225513 restraints weight = 20661.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.227978 restraints weight = 17524.370| |-----------------------------------------------------------------------------| r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4756 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6848 Z= 0.186 Angle : 0.584 6.945 9278 Z= 0.312 Chirality : 0.043 0.160 1024 Planarity : 0.004 0.042 1122 Dihedral : 4.704 20.784 872 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 1.19 (0.31), residues: 772 helix: 1.20 (0.23), residues: 472 sheet: -0.20 (0.65), residues: 66 loop : 0.50 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 121 HIS 0.003 0.001 HIS A 76 PHE 0.025 0.001 PHE A 107 TYR 0.021 0.002 TYR B 77 ARG 0.005 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 110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7114 (ttp-170) cc_final: 0.6793 (ttp-170) REVERT: A 79 TYR cc_start: 0.8107 (t80) cc_final: 0.7790 (t80) REVERT: A 92 ARG cc_start: 0.4812 (tpt170) cc_final: 0.4494 (mmt-90) REVERT: A 147 LYS cc_start: 0.6883 (pttt) cc_final: 0.6666 (pttt) REVERT: A 190 MET cc_start: 0.7891 (ttt) cc_final: 0.7581 (ttt) REVERT: B 73 ARG cc_start: 0.2725 (tpt170) cc_final: 0.2338 (tpt170) REVERT: B 121 TRP cc_start: 0.7099 (m-90) cc_final: 0.6466 (m-90) REVERT: B 263 MET cc_start: 0.0585 (mmp) cc_final: -0.0657 (mmm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1731 time to fit residues: 26.4418 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 : 0.720 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.5320 r_free = 0.5320 target = 0.312019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.302141 restraints weight = 31122.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.303257 restraints weight = 21317.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5313 r_free = 0.5313 target = 0.303982 restraints weight = 15641.484| |-----------------------------------------------------------------------------| r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4249 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6848 Z= 0.176 Angle : 0.575 7.511 9278 Z= 0.307 Chirality : 0.043 0.189 1024 Planarity : 0.004 0.037 1122 Dihedral : 4.655 19.786 872 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 1.29 (0.31), residues: 772 helix: 1.28 (0.23), residues: 472 sheet: -0.16 (0.66), residues: 66 loop : 0.54 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 121 HIS 0.003 0.001 HIS A 76 PHE 0.011 0.001 PHE B 332 TYR 0.014 0.001 TYR A 418 ARG 0.005 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 114 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8518 (mp10) cc_final: 0.7898 (mt0) REVERT: A 79 TYR cc_start: 0.7225 (t80) cc_final: 0.6677 (t80) REVERT: A 92 ARG cc_start: 0.5386 (tpt170) cc_final: 0.4491 (mmt-90) REVERT: A 190 MET cc_start: 0.7738 (ttt) cc_final: 0.7479 (ttt) REVERT: B 73 ARG cc_start: 0.4179 (tpt170) cc_final: 0.3833 (tpt170) REVERT: B 79 TYR cc_start: 0.6972 (t80) cc_final: 0.6685 (t80) REVERT: B 121 TRP cc_start: 0.6497 (m-90) cc_final: 0.5971 (m-90) REVERT: B 263 MET cc_start: 0.0171 (mmp) cc_final: -0.1088 (mmm) REVERT: B 273 LYS cc_start: 0.4932 (mttt) cc_final: 0.4504 (tttt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1705 time to fit residues: 26.3171 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 : 0.740 ------------------------------------------------------------------------------- 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: 3.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- 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 = 0.5044 r_free = 0.5044 target = 0.258564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.229070 restraints weight = 22949.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.228713 restraints weight = 19153.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.230551 restraints weight = 16871.816| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4752 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6848 Z= 0.192 Angle : 0.599 7.280 9278 Z= 0.318 Chirality : 0.043 0.180 1024 Planarity : 0.004 0.043 1122 Dihedral : 4.748 20.041 872 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: 1.21 (0.31), residues: 772 helix: 1.20 (0.23), residues: 472 sheet: -0.30 (0.64), residues: 66 loop : 0.58 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 121 HIS 0.003 0.001 HIS B 137 PHE 0.013 0.001 PHE B 332 TYR 0.015 0.001 TYR A 418 ARG 0.006 0.000 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.62 seconds wall clock time: 47 minutes 30.00 seconds (2850.00 seconds total)