Starting phenix.real_space_refine on Sat May 10 21:52:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8h_36070/05_2025/8j8h_36070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8h_36070/05_2025/8j8h_36070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8h_36070/05_2025/8j8h_36070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8h_36070/05_2025/8j8h_36070.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8h_36070/05_2025/8j8h_36070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8h_36070/05_2025/8j8h_36070.cif" } resolution = 3.4 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 4316 2.51 5 N 1167 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6868 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3651 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 1 Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2421 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain: "E" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 403 Classifications: {'DNA': 13, 'RNA': 7} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.78, per 1000 atoms: 0.70 Number of scatterers: 6868 At special positions: 0 Unit cell: (84, 79.8, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 39 15.00 Mg 1 11.99 O 1327 8.00 N 1167 7.00 C 4316 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: 1.83 Conformation dependent library (CDL) restraints added in 828.8 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 11 sheets defined 31.8% alpha, 15.6% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.747A pdb=" N ALA A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 removed outlier: 3.641A pdb=" N LYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.546A pdb=" N ILE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.050A pdb=" N TYR A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.496A pdb=" N ARG A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.188A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.591A pdb=" N VAL A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 4.211A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.899A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.597A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.510A pdb=" N PHE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.510A pdb=" N GLY B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.562A pdb=" N PHE B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 282 removed outlier: 7.119A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A 412 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU A 3 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS A 2 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.892A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 5.827A pdb=" N SER A 41 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.684A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.532A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'B' and resid 390 through 394 197 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1718 1.33 - 1.45: 1554 1.45 - 1.57: 3745 1.57 - 1.69: 77 1.69 - 1.81: 28 Bond restraints: 7122 Sorted by residual: bond pdb=" CB PRO B 419 " pdb=" CG PRO B 419 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" CB PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.00e+00 bond pdb=" CG PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 1.503 1.455 0.048 3.40e-02 8.65e+02 1.99e+00 bond pdb=" CB ASP B 346 " pdb=" CG ASP B 346 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.57e+00 bond pdb=" C SER B 180 " pdb=" N PHE B 181 " ideal model delta sigma weight residual 1.333 1.301 0.031 2.74e-02 1.33e+03 1.32e+00 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 9697 2.91 - 5.82: 76 5.82 - 8.73: 9 8.73 - 11.64: 2 11.64 - 14.55: 3 Bond angle restraints: 9787 Sorted by residual: angle pdb=" CA PRO B 419 " pdb=" N PRO B 419 " pdb=" CD PRO B 419 " ideal model delta sigma weight residual 112.00 99.90 12.10 1.40e+00 5.10e-01 7.47e+01 angle pdb=" CA PRO A 241 " pdb=" N PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 112.00 105.55 6.45 1.40e+00 5.10e-01 2.12e+01 angle pdb=" CA LEU A 394 " pdb=" CB LEU A 394 " pdb=" CG LEU A 394 " ideal model delta sigma weight residual 116.30 130.85 -14.55 3.50e+00 8.16e-02 1.73e+01 angle pdb=" N PRO A 241 " pdb=" CD PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 103.20 97.08 6.12 1.50e+00 4.44e-01 1.67e+01 angle pdb=" CA LEU A 215 " pdb=" CB LEU A 215 " pdb=" CG LEU A 215 " ideal model delta sigma weight residual 116.30 129.09 -12.79 3.50e+00 8.16e-02 1.34e+01 ... (remaining 9782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.87: 3797 28.87 - 57.75: 384 57.75 - 86.62: 29 86.62 - 115.49: 2 115.49 - 144.37: 3 Dihedral angle restraints: 4215 sinusoidal: 2047 harmonic: 2168 Sorted by residual: dihedral pdb=" C4' DA F 9 " pdb=" C3' DA F 9 " pdb=" O3' DA F 9 " pdb=" P A DG F 10 " ideal model delta sinusoidal sigma weight residual 220.00 75.63 144.37 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA LYS B 328 " pdb=" C LYS B 328 " pdb=" N LEU B 329 " pdb=" CA LEU B 329 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C4' DA F 16 " pdb=" C3' DA F 16 " pdb=" O3' DA F 16 " pdb=" P DG F 17 " ideal model delta sinusoidal sigma weight residual 220.00 82.66 137.34 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 4212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 857 0.054 - 0.108: 163 0.108 - 0.162: 25 0.162 - 0.215: 1 0.215 - 0.269: 4 Chirality restraints: 1050 Sorted by residual: chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1' U E 17 " pdb=" O4' U E 17 " pdb=" C2' U E 17 " pdb=" N1 U E 17 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' U E 1 " pdb=" O4' U E 1 " pdb=" C2' U E 1 " pdb=" N1 U E 1 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1047 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 418 " 0.056 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 419 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 419 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 419 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 240 " -0.040 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 241 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 320 " -0.014 2.00e-02 2.50e+03 1.33e-02 4.41e+00 pdb=" CG TRP A 320 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 320 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 320 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 320 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 320 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 320 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 320 " -0.001 2.00e-02 2.50e+03 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 81 2.51 - 3.11: 5082 3.11 - 3.71: 11814 3.71 - 4.30: 15642 4.30 - 4.90: 24702 Nonbonded interactions: 57321 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG A 601 " model vdw 1.914 2.170 nonbonded pdb=" ND2 ASN A 468 " pdb="MG MG A 601 " model vdw 2.096 2.250 nonbonded pdb=" OG SER A 11 " pdb=" O CYS A 20 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASN A 468 " pdb="MG MG A 601 " model vdw 2.238 2.170 nonbonded pdb=" O TYR A 328 " pdb=" ND1 HIS A 329 " model vdw 2.254 3.120 ... (remaining 57316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.60 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.070 Process input model: 21.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 7122 Z= 0.142 Angle : 0.694 14.547 9787 Z= 0.335 Chirality : 0.045 0.269 1050 Planarity : 0.005 0.079 1106 Dihedral : 20.214 144.365 2817 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.61 % Allowed : 33.69 % Favored : 65.71 % 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: -1.54 (0.31), residues: 732 helix: -0.66 (0.39), residues: 185 sheet: -0.98 (0.44), residues: 140 loop : -1.17 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 320 HIS 0.003 0.000 HIS A 217 PHE 0.017 0.001 PHE B 411 TYR 0.017 0.001 TYR B 416 ARG 0.002 0.000 ARG B 201 Details of bonding type rmsd hydrogen bonds : bond 0.27968 ( 213) hydrogen bonds : angle 9.20553 ( 578) covalent geometry : bond 0.00377 ( 7122) covalent geometry : angle 0.69412 ( 9787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.1404 time to fit residues: 17.7171 Evaluate side-chains 83 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain B residue 349 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0030 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN B 349 ASN B 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.106756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086014 restraints weight = 19195.824| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 5.09 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7122 Z= 0.167 Angle : 0.676 11.397 9787 Z= 0.334 Chirality : 0.047 0.275 1050 Planarity : 0.004 0.047 1106 Dihedral : 18.756 143.678 1280 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.46 % Allowed : 27.92 % Favored : 66.62 % 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: -1.79 (0.29), residues: 732 helix: -0.98 (0.32), residues: 211 sheet: -0.93 (0.43), residues: 142 loop : -1.36 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 320 HIS 0.003 0.001 HIS A 207 PHE 0.017 0.001 PHE B 411 TYR 0.021 0.001 TYR A 104 ARG 0.004 0.001 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 213) hydrogen bonds : angle 5.94108 ( 578) covalent geometry : bond 0.00385 ( 7122) covalent geometry : angle 0.67619 ( 9787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7663 (mtt180) REVERT: A 289 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: A 436 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6593 (mm-30) REVERT: A 444 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 476 GLU cc_start: 0.7943 (pm20) cc_final: 0.7618 (pm20) REVERT: B 191 ASP cc_start: 0.8731 (t0) cc_final: 0.8470 (t0) REVERT: B 336 MET cc_start: 0.7690 (tpp) cc_final: 0.7442 (tpp) outliers start: 36 outliers final: 18 residues processed: 108 average time/residue: 0.1634 time to fit residues: 24.5701 Evaluate side-chains 101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086166 restraints weight = 19200.415| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.04 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7122 Z= 0.138 Angle : 0.654 11.619 9787 Z= 0.315 Chirality : 0.047 0.282 1050 Planarity : 0.004 0.044 1106 Dihedral : 18.550 143.023 1277 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.40 % Allowed : 27.77 % Favored : 67.83 % 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: -1.77 (0.29), residues: 732 helix: -0.83 (0.33), residues: 212 sheet: -1.00 (0.44), residues: 140 loop : -1.39 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.019 0.001 PHE B 411 TYR 0.019 0.001 TYR A 104 ARG 0.002 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 213) hydrogen bonds : angle 5.52629 ( 578) covalent geometry : bond 0.00315 ( 7122) covalent geometry : angle 0.65365 ( 9787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6606 (pmm) cc_final: 0.6356 (pmm) REVERT: A 289 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: A 436 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6138 (mm-30) REVERT: A 444 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 476 GLU cc_start: 0.7953 (pm20) cc_final: 0.7581 (pm20) outliers start: 29 outliers final: 19 residues processed: 106 average time/residue: 0.1479 time to fit residues: 22.4511 Evaluate side-chains 101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN B 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.102709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081300 restraints weight = 20013.879| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 5.18 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7122 Z= 0.263 Angle : 0.719 12.734 9787 Z= 0.353 Chirality : 0.048 0.266 1050 Planarity : 0.004 0.043 1106 Dihedral : 18.727 145.144 1277 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.98 % Allowed : 24.58 % Favored : 68.44 % 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: -1.89 (0.30), residues: 732 helix: -0.86 (0.33), residues: 212 sheet: -1.24 (0.44), residues: 143 loop : -1.43 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.020 0.002 PHE B 411 TYR 0.020 0.002 TYR A 104 ARG 0.003 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 213) hydrogen bonds : angle 5.50573 ( 578) covalent geometry : bond 0.00592 ( 7122) covalent geometry : angle 0.71886 ( 9787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7545 (mtt180) REVERT: A 289 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: A 368 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8757 (pp20) REVERT: A 436 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6233 (mm-30) REVERT: A 444 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 476 GLU cc_start: 0.7925 (pm20) cc_final: 0.7454 (pm20) REVERT: B 191 ASP cc_start: 0.8862 (t0) cc_final: 0.8606 (t0) REVERT: B 328 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8645 (mtmm) REVERT: B 402 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8752 (mm) outliers start: 46 outliers final: 29 residues processed: 114 average time/residue: 0.1633 time to fit residues: 26.0306 Evaluate side-chains 111 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.105467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.084774 restraints weight = 19207.790| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.98 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.149 Angle : 0.662 12.872 9787 Z= 0.320 Chirality : 0.047 0.287 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.567 144.213 1277 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.77 % Allowed : 27.01 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.30), residues: 732 helix: -0.69 (0.34), residues: 211 sheet: -1.32 (0.44), residues: 135 loop : -1.38 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 320 HIS 0.002 0.001 HIS B 320 PHE 0.021 0.001 PHE B 411 TYR 0.020 0.001 TYR A 104 ARG 0.002 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 213) hydrogen bonds : angle 5.26390 ( 578) covalent geometry : bond 0.00347 ( 7122) covalent geometry : angle 0.66222 ( 9787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6657 (pmm) cc_final: 0.6449 (pmm) REVERT: A 289 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: A 368 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8733 (pp20) REVERT: A 436 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6227 (mm-30) REVERT: A 444 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 476 GLU cc_start: 0.8061 (pm20) cc_final: 0.7551 (pm20) REVERT: A 505 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (p90) REVERT: B 274 GLU cc_start: 0.8820 (mp0) cc_final: 0.8558 (mp0) outliers start: 38 outliers final: 20 residues processed: 110 average time/residue: 0.1523 time to fit residues: 24.3453 Evaluate side-chains 104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.107167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.086445 restraints weight = 19217.641| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 5.03 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.135 Angle : 0.655 12.246 9787 Z= 0.315 Chirality : 0.046 0.289 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.496 143.275 1277 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.55 % Allowed : 28.22 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.30), residues: 732 helix: -0.58 (0.34), residues: 211 sheet: -1.38 (0.44), residues: 135 loop : -1.32 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.014 0.001 PHE B 411 TYR 0.019 0.001 TYR A 104 ARG 0.002 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 213) hydrogen bonds : angle 5.15964 ( 578) covalent geometry : bond 0.00313 ( 7122) covalent geometry : angle 0.65534 ( 9787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.6614 (pmm) cc_final: 0.6384 (pmm) REVERT: A 289 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: A 436 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6285 (mm-30) REVERT: A 444 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 476 GLU cc_start: 0.8098 (pm20) cc_final: 0.7650 (pm20) REVERT: A 505 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7947 (p90) REVERT: B 191 ASP cc_start: 0.8873 (t0) cc_final: 0.8618 (t0) REVERT: B 262 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: B 328 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8525 (mtmm) outliers start: 30 outliers final: 16 residues processed: 108 average time/residue: 0.1785 time to fit residues: 26.9910 Evaluate side-chains 102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** 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 = 0.3849 r_free = 0.3849 target = 0.106145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084680 restraints weight = 19462.409| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 5.22 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7122 Z= 0.155 Angle : 0.677 13.998 9787 Z= 0.326 Chirality : 0.047 0.285 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.525 143.118 1277 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.40 % Allowed : 30.20 % Favored : 65.40 % 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: -1.70 (0.30), residues: 732 helix: -0.62 (0.34), residues: 212 sheet: -1.26 (0.45), residues: 133 loop : -1.32 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 320 HIS 0.002 0.001 HIS B 320 PHE 0.022 0.001 PHE B 411 TYR 0.024 0.001 TYR B 416 ARG 0.001 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 213) hydrogen bonds : angle 5.12526 ( 578) covalent geometry : bond 0.00363 ( 7122) covalent geometry : angle 0.67708 ( 9787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 436 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 444 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 476 GLU cc_start: 0.8110 (pm20) cc_final: 0.7650 (pm20) REVERT: A 505 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7907 (p90) REVERT: B 336 MET cc_start: 0.7649 (tpp) cc_final: 0.7240 (mmt) outliers start: 29 outliers final: 19 residues processed: 99 average time/residue: 0.1533 time to fit residues: 21.8204 Evaluate side-chains 99 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 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 = 0.3848 r_free = 0.3848 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084552 restraints weight = 19537.063| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 5.26 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7122 Z= 0.160 Angle : 0.679 14.433 9787 Z= 0.327 Chirality : 0.046 0.288 1050 Planarity : 0.004 0.039 1106 Dihedral : 18.586 142.881 1277 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.25 % Allowed : 30.65 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.30), residues: 732 helix: -0.60 (0.34), residues: 209 sheet: -1.24 (0.46), residues: 133 loop : -1.31 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 320 HIS 0.002 0.000 HIS B 320 PHE 0.014 0.001 PHE B 411 TYR 0.017 0.001 TYR A 104 ARG 0.001 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 213) hydrogen bonds : angle 5.10407 ( 578) covalent geometry : bond 0.00371 ( 7122) covalent geometry : angle 0.67939 ( 9787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7759 (tpm170) REVERT: A 289 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: A 436 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6632 (mm-30) REVERT: A 444 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 476 GLU cc_start: 0.8117 (pm20) cc_final: 0.7798 (pm20) REVERT: A 505 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7918 (p90) REVERT: B 191 ASP cc_start: 0.8902 (t0) cc_final: 0.8650 (t0) REVERT: B 336 MET cc_start: 0.7666 (tpp) cc_final: 0.7305 (mmm) outliers start: 28 outliers final: 21 residues processed: 98 average time/residue: 0.1758 time to fit residues: 23.8528 Evaluate side-chains 102 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 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 = 0.3861 r_free = 0.3861 target = 0.107206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086570 restraints weight = 19301.351| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 5.04 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.139 Angle : 0.675 14.293 9787 Z= 0.325 Chirality : 0.046 0.299 1050 Planarity : 0.004 0.039 1106 Dihedral : 18.608 142.050 1277 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.49 % Allowed : 31.11 % Favored : 65.40 % 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: -1.65 (0.30), residues: 732 helix: -0.54 (0.34), residues: 209 sheet: -1.20 (0.46), residues: 133 loop : -1.33 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.013 0.001 PHE B 411 TYR 0.022 0.001 TYR B 416 ARG 0.002 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 213) hydrogen bonds : angle 5.06336 ( 578) covalent geometry : bond 0.00327 ( 7122) covalent geometry : angle 0.67450 ( 9787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 436 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6658 (mm-30) REVERT: A 444 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 476 GLU cc_start: 0.8125 (pm20) cc_final: 0.7633 (pm20) REVERT: A 505 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7961 (p90) REVERT: B 336 MET cc_start: 0.7589 (tpp) cc_final: 0.7154 (mmt) outliers start: 23 outliers final: 20 residues processed: 98 average time/residue: 0.1484 time to fit residues: 20.9532 Evaluate side-chains 105 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.108361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086764 restraints weight = 19813.402| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 5.34 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.131 Angle : 0.675 14.311 9787 Z= 0.324 Chirality : 0.046 0.300 1050 Planarity : 0.004 0.039 1106 Dihedral : 18.577 141.668 1277 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.79 % Allowed : 31.41 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.30), residues: 732 helix: -0.46 (0.34), residues: 209 sheet: -1.09 (0.47), residues: 131 loop : -1.28 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.013 0.001 PHE B 411 TYR 0.018 0.001 TYR B 416 ARG 0.002 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 213) hydrogen bonds : angle 5.02567 ( 578) covalent geometry : bond 0.00308 ( 7122) covalent geometry : angle 0.67506 ( 9787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TRP cc_start: 0.7941 (t60) cc_final: 0.7546 (t60) REVERT: A 99 GLU cc_start: 0.9534 (mm-30) cc_final: 0.8834 (pp20) REVERT: A 102 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7955 (tpm170) REVERT: A 139 TRP cc_start: 0.8348 (m100) cc_final: 0.7305 (m100) REVERT: A 213 ARG cc_start: 0.8252 (ptp-170) cc_final: 0.7784 (mtt180) REVERT: A 289 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: A 436 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6823 (mm-30) REVERT: A 444 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 476 GLU cc_start: 0.8115 (pm20) cc_final: 0.7673 (pm20) REVERT: A 505 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7898 (p90) REVERT: B 191 ASP cc_start: 0.8910 (t0) cc_final: 0.8664 (t0) REVERT: B 336 MET cc_start: 0.7573 (tpp) cc_final: 0.7174 (mmt) outliers start: 25 outliers final: 19 residues processed: 107 average time/residue: 0.1831 time to fit residues: 26.9743 Evaluate side-chains 107 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.0170 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 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 = 0.3867 r_free = 0.3867 target = 0.107748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087106 restraints weight = 19221.373| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.99 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7122 Z= 0.141 Angle : 0.683 14.902 9787 Z= 0.327 Chirality : 0.046 0.297 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.580 141.694 1277 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.34 % Allowed : 31.71 % Favored : 64.95 % 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: -1.53 (0.30), residues: 732 helix: -0.43 (0.34), residues: 209 sheet: -1.05 (0.47), residues: 131 loop : -1.28 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 320 HIS 0.002 0.000 HIS B 320 PHE 0.012 0.001 PHE B 411 TYR 0.019 0.001 TYR B 416 ARG 0.001 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 213) hydrogen bonds : angle 5.00885 ( 578) covalent geometry : bond 0.00333 ( 7122) covalent geometry : angle 0.68317 ( 9787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.83 seconds wall clock time: 48 minutes 59.54 seconds (2939.54 seconds total)