Starting phenix.real_space_refine on Wed Sep 17 07:06:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1j_13162/09_2025/7p1j_13162.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1j_13162/09_2025/7p1j_13162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p1j_13162/09_2025/7p1j_13162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1j_13162/09_2025/7p1j_13162.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1j_13162/09_2025/7p1j_13162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1j_13162/09_2025/7p1j_13162.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4334 2.51 5 N 1034 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6502 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3251 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 1 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3251 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.28 Number of scatterers: 6502 At special positions: 0 Unit cell: (119.312, 90.2625, 85.075, 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 1096 8.00 N 1034 7.00 C 4334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 362.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 80 through 104 removed outlier: 4.203A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.216A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.490A pdb=" N GLY B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 190 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 200 through 223 Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.147A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.057A pdb=" N LEU B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.664A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 Processing helix chain 'B' and resid 360 through 377 removed outlier: 3.966A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 3.561A pdb=" N LYS B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 417 through 439 Processing helix chain 'B' and resid 446 through 455 removed outlier: 3.888A pdb=" N ILE B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 478 removed outlier: 4.214A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 516 removed outlier: 3.529A pdb=" N ALA B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 513 - end of helix removed outlier: 3.714A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 105 removed outlier: 4.099A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.207A pdb=" N GLY A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 4.392A pdb=" N GLY A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.961A pdb=" N ASN A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 191 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 200 through 223 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.688A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.550A pdb=" N GLY A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 293 removed outlier: 4.238A pdb=" N SER A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.806A pdb=" N PHE A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.501A pdb=" N PHE A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.015A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 4.250A pdb=" N VAL A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 417 through 439 removed outlier: 3.527A pdb=" N VAL A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.942A pdb=" N ILE A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.000A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 516 removed outlier: 3.614A pdb=" N ALA A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Proline residue: A 502 - end of helix Proline residue: A 513 - end of helix removed outlier: 3.704A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.62 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: 1966 1.34 - 1.46: 1378 1.46 - 1.58: 3244 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6646 Sorted by residual: bond pdb=" N VAL B 158 " pdb=" CA VAL B 158 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 8.11e-01 bond pdb=" C TYR A 325 " pdb=" N PHE A 326 " ideal model delta sigma weight residual 1.332 1.344 -0.011 1.50e-02 4.44e+03 5.57e-01 bond pdb=" CA LEU A 208 " pdb=" C LEU A 208 " ideal model delta sigma weight residual 1.519 1.527 -0.008 1.22e-02 6.72e+03 4.58e-01 bond pdb=" C PHE A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.04e-01 bond pdb=" N VAL A 158 " pdb=" CA VAL A 158 " ideal model delta sigma weight residual 1.461 1.454 0.007 1.23e-02 6.61e+03 3.42e-01 ... (remaining 6641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 8933 1.73 - 3.47: 97 3.47 - 5.20: 17 5.20 - 6.93: 3 6.93 - 8.66: 2 Bond angle restraints: 9052 Sorted by residual: angle pdb=" C VAL A 248 " pdb=" N VAL A 249 " pdb=" CA VAL A 249 " ideal model delta sigma weight residual 120.33 122.82 -2.49 8.00e-01 1.56e+00 9.68e+00 angle pdb=" CA LEU B 412 " pdb=" CB LEU B 412 " pdb=" CG LEU B 412 " ideal model delta sigma weight residual 116.30 124.96 -8.66 3.50e+00 8.16e-02 6.13e+00 angle pdb=" CA LEU A 412 " pdb=" CB LEU A 412 " pdb=" CG LEU A 412 " ideal model delta sigma weight residual 116.30 124.94 -8.64 3.50e+00 8.16e-02 6.09e+00 angle pdb=" C ALA A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C VAL A 249 " pdb=" CA VAL A 249 " pdb=" CB VAL A 249 " ideal model delta sigma weight residual 114.00 111.22 2.78 1.31e+00 5.83e-01 4.51e+00 ... (remaining 9047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 3577 11.46 - 22.92: 186 22.92 - 34.38: 62 34.38 - 45.84: 28 45.84 - 57.30: 5 Dihedral angle restraints: 3858 sinusoidal: 1436 harmonic: 2422 Sorted by residual: dihedral pdb=" N ARG A 176 " pdb=" CA ARG A 176 " pdb=" CB ARG A 176 " pdb=" CG ARG A 176 " ideal model delta sinusoidal sigma weight residual -60.00 -117.30 57.30 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N PHE A 356 " pdb=" CA PHE A 356 " pdb=" CB PHE A 356 " pdb=" CG PHE A 356 " ideal model delta sinusoidal sigma weight residual -180.00 -127.72 -52.28 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" N TRP A 171 " pdb=" CA TRP A 171 " pdb=" CB TRP A 171 " pdb=" CG TRP A 171 " ideal model delta sinusoidal sigma weight residual -60.00 -108.02 48.02 3 1.50e+01 4.44e-03 8.58e+00 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 661 0.023 - 0.045: 245 0.045 - 0.068: 152 0.068 - 0.090: 35 0.090 - 0.113: 25 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CG LEU A 412 " pdb=" CB LEU A 412 " pdb=" CD1 LEU A 412 " pdb=" CD2 LEU A 412 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.11e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.01e-01 ... (remaining 1115 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 512 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 513 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 109 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 110 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 512 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 513 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 513 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 513 " -0.017 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1902 2.82 - 3.34: 6870 3.34 - 3.86: 10382 3.86 - 4.38: 10917 4.38 - 4.90: 19952 Nonbonded interactions: 50023 Sorted by model distance: nonbonded pdb=" O PHE A 153 " pdb=" ND2 ASN A 157 " model vdw 2.305 3.120 nonbonded pdb=" O PHE A 444 " pdb=" NZ LYS A 449 " model vdw 2.314 3.120 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.315 3.120 nonbonded pdb=" OG SER B 106 " pdb=" OE1 GLU B 107 " model vdw 2.322 3.040 nonbonded pdb=" O PHE B 153 " pdb=" ND2 ASN B 157 " model vdw 2.372 3.120 ... (remaining 50018 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: 0.01 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 0.018 6646 Z= 0.090 Angle : 0.476 8.663 9052 Z= 0.238 Chirality : 0.034 0.113 1118 Planarity : 0.003 0.042 1094 Dihedral : 8.895 57.299 2314 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 7.45 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.30), residues: 860 helix: 2.30 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.03 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 413 TYR 0.004 0.001 TYR B 436 PHE 0.004 0.001 PHE B 358 TRP 0.006 0.001 TRP A 392 HIS 0.001 0.000 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 6646) covalent geometry : angle 0.47607 ( 9052) hydrogen bonds : bond 0.20953 ( 498) hydrogen bonds : angle 5.50645 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 TRP cc_start: 0.7497 (t60) cc_final: 0.7247 (t-100) REVERT: B 165 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (mp) REVERT: B 214 GLU cc_start: 0.8011 (tt0) cc_final: 0.7423 (tp30) REVERT: B 440 CYS cc_start: 0.7345 (p) cc_final: 0.6981 (m) REVERT: B 454 PHE cc_start: 0.8504 (m-10) cc_final: 0.8273 (m-80) REVERT: A 433 LEU cc_start: 0.8977 (mm) cc_final: 0.8735 (mm) outliers start: 16 outliers final: 2 residues processed: 242 average time/residue: 0.0672 time to fit residues: 22.6909 Evaluate side-chains 133 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain A residue 226 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** 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 = 0.4197 r_free = 0.4197 target = 0.097749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.081961 restraints weight = 30229.563| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 4.86 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6646 Z= 0.173 Angle : 0.803 11.611 9052 Z= 0.381 Chirality : 0.045 0.361 1118 Planarity : 0.005 0.082 1094 Dihedral : 4.006 31.504 910 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.58 % Allowed : 19.48 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.30), residues: 860 helix: 2.25 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 431 TYR 0.008 0.001 TYR A 325 PHE 0.014 0.002 PHE B 322 TRP 0.019 0.002 TRP B 377 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6646) covalent geometry : angle 0.80265 ( 9052) hydrogen bonds : bond 0.05261 ( 498) hydrogen bonds : angle 4.13022 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 277 ASP cc_start: 0.8745 (t70) cc_final: 0.8448 (t0) REVERT: B 322 PHE cc_start: 0.8369 (m-10) cc_final: 0.8047 (m-80) REVERT: B 454 PHE cc_start: 0.8552 (m-10) cc_final: 0.8195 (m-80) REVERT: B 466 ILE cc_start: 0.9372 (mt) cc_final: 0.9109 (tt) REVERT: A 326 PHE cc_start: 0.7377 (m-80) cc_final: 0.7122 (m-80) REVERT: A 332 ASP cc_start: 0.8296 (t0) cc_final: 0.8080 (t0) REVERT: A 433 LEU cc_start: 0.9132 (mm) cc_final: 0.8917 (mm) REVERT: A 454 PHE cc_start: 0.8576 (m-10) cc_final: 0.8341 (m-80) REVERT: A 490 LEU cc_start: 0.8709 (mt) cc_final: 0.8399 (mt) outliers start: 32 outliers final: 21 residues processed: 168 average time/residue: 0.0592 time to fit residues: 14.6275 Evaluate side-chains 139 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 356 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** 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 = 0.4183 r_free = 0.4183 target = 0.097217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.081363 restraints weight = 31155.543| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 4.74 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6646 Z= 0.169 Angle : 0.794 13.415 9052 Z= 0.368 Chirality : 0.044 0.273 1118 Planarity : 0.004 0.050 1094 Dihedral : 4.323 30.352 910 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.87 % Allowed : 19.48 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.30), residues: 860 helix: 1.83 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.26 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 431 TYR 0.010 0.001 TYR B 485 PHE 0.019 0.002 PHE A 322 TRP 0.009 0.001 TRP A 392 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6646) covalent geometry : angle 0.79377 ( 9052) hydrogen bonds : bond 0.04581 ( 498) hydrogen bonds : angle 4.17681 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 288 CYS cc_start: 0.8360 (t) cc_final: 0.8084 (t) REVERT: B 454 PHE cc_start: 0.8521 (m-10) cc_final: 0.8141 (m-80) REVERT: B 466 ILE cc_start: 0.9339 (mt) cc_final: 0.9032 (tt) REVERT: A 122 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6544 (t80) REVERT: A 332 ASP cc_start: 0.8348 (t0) cc_final: 0.8105 (t0) REVERT: A 433 LEU cc_start: 0.9130 (mm) cc_final: 0.8872 (mm) REVERT: A 454 PHE cc_start: 0.8546 (m-10) cc_final: 0.8333 (m-80) outliers start: 41 outliers final: 25 residues processed: 148 average time/residue: 0.0583 time to fit residues: 12.8895 Evaluate side-chains 144 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 356 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** 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 = 0.4192 r_free = 0.4192 target = 0.097249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.081345 restraints weight = 30914.542| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 5.01 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6646 Z= 0.136 Angle : 0.736 10.548 9052 Z= 0.341 Chirality : 0.042 0.293 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.302 29.897 910 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.16 % Allowed : 19.34 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.29), residues: 860 helix: 1.74 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.20 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 431 TYR 0.016 0.001 TYR A 260 PHE 0.011 0.001 PHE A 285 TRP 0.011 0.001 TRP B 377 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6646) covalent geometry : angle 0.73610 ( 9052) hydrogen bonds : bond 0.04084 ( 498) hydrogen bonds : angle 4.01813 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8493 (tt0) cc_final: 0.7608 (tp30) REVERT: B 252 MET cc_start: 0.8084 (ttm) cc_final: 0.7764 (ttm) REVERT: B 271 MET cc_start: 0.8416 (ppp) cc_final: 0.8119 (ppp) REVERT: B 288 CYS cc_start: 0.8357 (t) cc_final: 0.8148 (t) REVERT: B 454 PHE cc_start: 0.8468 (m-10) cc_final: 0.8069 (m-80) REVERT: A 122 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6557 (t80) REVERT: A 131 PHE cc_start: 0.8433 (m-10) cc_final: 0.8228 (m-10) REVERT: A 332 ASP cc_start: 0.8316 (t0) cc_final: 0.8100 (t0) REVERT: A 433 LEU cc_start: 0.9142 (mm) cc_final: 0.8878 (mm) REVERT: A 454 PHE cc_start: 0.8583 (m-10) cc_final: 0.8261 (m-80) outliers start: 36 outliers final: 25 residues processed: 148 average time/residue: 0.0594 time to fit residues: 13.0387 Evaluate side-chains 133 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.097059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.082665 restraints weight = 31476.942| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 4.51 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6646 Z= 0.135 Angle : 0.760 14.180 9052 Z= 0.350 Chirality : 0.042 0.266 1118 Planarity : 0.004 0.040 1094 Dihedral : 4.314 29.829 910 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.87 % Allowed : 20.49 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.30), residues: 860 helix: 1.60 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.26 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR B 260 PHE 0.009 0.001 PHE B 285 TRP 0.013 0.001 TRP B 377 HIS 0.002 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6646) covalent geometry : angle 0.76042 ( 9052) hydrogen bonds : bond 0.03957 ( 498) hydrogen bonds : angle 3.97946 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 165 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 214 GLU cc_start: 0.8512 (tt0) cc_final: 0.7630 (tp30) REVERT: B 235 MET cc_start: 0.8222 (mmt) cc_final: 0.8007 (mmt) REVERT: B 454 PHE cc_start: 0.8415 (m-10) cc_final: 0.8026 (m-80) REVERT: A 122 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 235 MET cc_start: 0.6609 (mtt) cc_final: 0.6151 (mtt) REVERT: A 332 ASP cc_start: 0.8151 (t0) cc_final: 0.7904 (t0) REVERT: A 433 LEU cc_start: 0.9091 (mm) cc_final: 0.8762 (mm) REVERT: A 454 PHE cc_start: 0.8402 (m-10) cc_final: 0.8138 (m-80) outliers start: 41 outliers final: 23 residues processed: 141 average time/residue: 0.0648 time to fit residues: 13.2217 Evaluate side-chains 133 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.097430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.081200 restraints weight = 31282.337| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 4.96 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6646 Z= 0.142 Angle : 0.783 18.257 9052 Z= 0.361 Chirality : 0.041 0.203 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.337 30.122 910 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.87 % Allowed : 21.35 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.30), residues: 860 helix: 1.52 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.27 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.014 0.001 TYR A 260 PHE 0.013 0.001 PHE B 358 TRP 0.013 0.001 TRP B 377 HIS 0.002 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6646) covalent geometry : angle 0.78268 ( 9052) hydrogen bonds : bond 0.03887 ( 498) hydrogen bonds : angle 4.02612 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8635 (tt0) cc_final: 0.7634 (tp30) REVERT: B 377 TRP cc_start: 0.7331 (t-100) cc_final: 0.7041 (t-100) REVERT: B 454 PHE cc_start: 0.8426 (m-10) cc_final: 0.8022 (m-80) REVERT: B 485 TYR cc_start: 0.9041 (m-80) cc_final: 0.8731 (m-80) REVERT: A 122 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6921 (t80) REVERT: A 235 MET cc_start: 0.7349 (mtt) cc_final: 0.7147 (mtt) REVERT: A 332 ASP cc_start: 0.8542 (t0) cc_final: 0.8288 (t0) REVERT: A 424 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8282 (mt) REVERT: A 433 LEU cc_start: 0.9276 (mm) cc_final: 0.8951 (mm) REVERT: A 454 PHE cc_start: 0.8875 (m-10) cc_final: 0.8414 (m-80) outliers start: 41 outliers final: 26 residues processed: 139 average time/residue: 0.0604 time to fit residues: 12.3944 Evaluate side-chains 134 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** 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 = 0.4185 r_free = 0.4185 target = 0.097086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.082494 restraints weight = 31540.773| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 4.30 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6646 Z= 0.147 Angle : 0.784 12.529 9052 Z= 0.368 Chirality : 0.042 0.199 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.426 30.199 910 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.30 % Allowed : 21.49 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.30), residues: 860 helix: 1.46 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.22 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.017 0.002 TYR A 260 PHE 0.015 0.001 PHE B 451 TRP 0.010 0.001 TRP A 392 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6646) covalent geometry : angle 0.78365 ( 9052) hydrogen bonds : bond 0.03915 ( 498) hydrogen bonds : angle 4.06903 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 MET cc_start: 0.8195 (mtm) cc_final: 0.7976 (mpp) REVERT: B 214 GLU cc_start: 0.8571 (tt0) cc_final: 0.7648 (tp30) REVERT: B 377 TRP cc_start: 0.6780 (t-100) cc_final: 0.6450 (t-100) REVERT: B 454 PHE cc_start: 0.8455 (m-10) cc_final: 0.8030 (m-80) REVERT: A 122 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6508 (t80) REVERT: A 424 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 433 LEU cc_start: 0.9128 (mm) cc_final: 0.8801 (mm) REVERT: A 454 PHE cc_start: 0.8462 (m-10) cc_final: 0.8164 (m-80) outliers start: 37 outliers final: 24 residues processed: 135 average time/residue: 0.0582 time to fit residues: 11.7627 Evaluate side-chains 133 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 51 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** 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 = 0.4194 r_free = 0.4194 target = 0.097590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.083051 restraints weight = 31817.024| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 4.37 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6646 Z= 0.133 Angle : 0.783 13.636 9052 Z= 0.367 Chirality : 0.041 0.197 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.383 29.649 910 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.58 % Allowed : 22.49 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.30), residues: 860 helix: 1.50 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.33 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.016 0.001 TYR A 260 PHE 0.020 0.001 PHE A 322 TRP 0.009 0.001 TRP B 232 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6646) covalent geometry : angle 0.78265 ( 9052) hydrogen bonds : bond 0.03854 ( 498) hydrogen bonds : angle 4.01339 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8565 (tt0) cc_final: 0.7614 (tp30) REVERT: B 377 TRP cc_start: 0.6785 (t-100) cc_final: 0.6450 (t-100) REVERT: B 454 PHE cc_start: 0.8434 (m-10) cc_final: 0.8007 (m-80) REVERT: A 122 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 291 MET cc_start: 0.7176 (ppp) cc_final: 0.6955 (ppp) REVERT: A 424 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 433 LEU cc_start: 0.9130 (mm) cc_final: 0.8819 (mm) REVERT: A 454 PHE cc_start: 0.8401 (m-10) cc_final: 0.8109 (m-80) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.0608 time to fit residues: 12.3800 Evaluate side-chains 134 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 5 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.098440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.083947 restraints weight = 31808.463| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 4.39 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6646 Z= 0.131 Angle : 0.804 13.738 9052 Z= 0.374 Chirality : 0.042 0.206 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.411 29.815 910 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.58 % Allowed : 23.93 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.30), residues: 860 helix: 1.49 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.45 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.019 0.001 TYR A 260 PHE 0.021 0.001 PHE A 322 TRP 0.009 0.001 TRP B 232 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6646) covalent geometry : angle 0.80370 ( 9052) hydrogen bonds : bond 0.03718 ( 498) hydrogen bonds : angle 4.03222 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8566 (tt0) cc_final: 0.7621 (tp30) REVERT: B 377 TRP cc_start: 0.6642 (t-100) cc_final: 0.6344 (t-100) REVERT: B 454 PHE cc_start: 0.8405 (m-10) cc_final: 0.7980 (m-80) REVERT: A 122 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6485 (t80) REVERT: A 291 MET cc_start: 0.7029 (ppp) cc_final: 0.6780 (ppp) REVERT: A 424 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 433 LEU cc_start: 0.9122 (mm) cc_final: 0.8817 (mm) REVERT: A 454 PHE cc_start: 0.8378 (m-10) cc_final: 0.8083 (m-80) REVERT: A 494 PHE cc_start: 0.8047 (m-80) cc_final: 0.7710 (m-80) outliers start: 25 outliers final: 21 residues processed: 131 average time/residue: 0.0608 time to fit residues: 11.7720 Evaluate side-chains 132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** 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 = 0.4198 r_free = 0.4198 target = 0.097990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.083623 restraints weight = 31458.250| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 4.22 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6646 Z= 0.136 Angle : 0.820 14.844 9052 Z= 0.387 Chirality : 0.043 0.216 1118 Planarity : 0.004 0.041 1094 Dihedral : 4.396 29.983 910 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.30 % Allowed : 24.21 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.30), residues: 860 helix: 1.45 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.39 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.019 0.001 TYR A 260 PHE 0.018 0.001 PHE A 322 TRP 0.009 0.001 TRP A 392 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6646) covalent geometry : angle 0.82011 ( 9052) hydrogen bonds : bond 0.03838 ( 498) hydrogen bonds : angle 4.10233 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 GLU cc_start: 0.8574 (tt0) cc_final: 0.7632 (tp30) REVERT: B 377 TRP cc_start: 0.6760 (t-100) cc_final: 0.6409 (t-100) REVERT: B 454 PHE cc_start: 0.8415 (m-10) cc_final: 0.8038 (m-80) REVERT: A 122 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6554 (t80) REVERT: A 291 MET cc_start: 0.7058 (ppp) cc_final: 0.6790 (ppp) REVERT: A 424 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 433 LEU cc_start: 0.9117 (mm) cc_final: 0.8798 (mm) REVERT: A 454 PHE cc_start: 0.8451 (m-10) cc_final: 0.8215 (m-80) outliers start: 30 outliers final: 23 residues processed: 131 average time/residue: 0.0573 time to fit residues: 11.1589 Evaluate side-chains 138 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 74 optimal weight: 0.0040 chunk 76 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.097420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.082870 restraints weight = 31750.296| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.20 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6646 Z= 0.150 Angle : 0.839 14.906 9052 Z= 0.397 Chirality : 0.043 0.248 1118 Planarity : 0.004 0.042 1094 Dihedral : 4.448 30.571 910 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.87 % Allowed : 24.79 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.30), residues: 860 helix: 1.41 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.37 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.020 0.001 TYR A 260 PHE 0.016 0.001 PHE A 322 TRP 0.010 0.001 TRP A 392 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6646) covalent geometry : angle 0.83881 ( 9052) hydrogen bonds : bond 0.03867 ( 498) hydrogen bonds : angle 4.23919 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1703.32 seconds wall clock time: 29 minutes 57.78 seconds (1797.78 seconds total)