Starting phenix.real_space_refine on Wed Mar 12 00:48:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8h_36070/03_2025/8j8h_36070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8h_36070/03_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_36070/03_2025/8j8h_36070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8h_36070/03_2025/8j8h_36070.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8h_36070/03_2025/8j8h_36070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8h_36070/03_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-5624/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: 4.57, per 1000 atoms: 0.67 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: 1.80 Conformation dependent library (CDL) restraints added in 836.4 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: 2.46 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: 2.61 Time building geometry restraints manager: 2.12 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- 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= 0.250 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 *********************** 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 : 0.763 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.1529 time to fit residues: 19.1558 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 : 0.696 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086012 restraints weight = 19195.825| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 5.10 r_work (final): 0.3442 ------------------------------------------------------------------------------- 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 = 0.60 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 = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- 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= 0.242 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 *********************** 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 : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7664 (mtt180) REVERT: A 289 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 436 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6593 (mm-30) REVERT: A 444 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 476 GLU cc_start: 0.7946 (pm20) cc_final: 0.7620 (pm20) REVERT: B 191 ASP cc_start: 0.8731 (t0) cc_final: 0.8470 (t0) REVERT: B 336 MET cc_start: 0.7689 (tpp) cc_final: 0.7441 (tpp) outliers start: 36 outliers final: 18 residues processed: 108 average time/residue: 0.1857 time to fit residues: 28.3029 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 : 0.721 ------------------------------------------------------------------------------- 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: 4.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 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: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082614 restraints weight = 19573.601| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.96 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7122 Z= 0.319 Angle : 0.696 11.645 9787 Z= 0.342 Chirality : 0.048 0.268 1050 Planarity : 0.004 0.045 1106 Dihedral : 18.689 144.486 1277 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.31 % Allowed : 26.71 % Favored : 67.98 % 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: -1.85 (0.29), residues: 732 helix: -0.87 (0.33), residues: 212 sheet: -1.26 (0.43), residues: 143 loop : -1.35 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 320 HIS 0.004 0.001 HIS A 217 PHE 0.021 0.002 PHE B 411 TYR 0.021 0.002 TYR A 104 ARG 0.003 0.000 ARG A 275 *********************** 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: 35 poor density : 82 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6777 (pmm) cc_final: 0.6538 (pmm) REVERT: A 95 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6836 (mm-30) REVERT: A 289 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: A 436 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6191 (mm-30) REVERT: A 444 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 476 GLU cc_start: 0.7932 (pm20) cc_final: 0.7544 (pm20) REVERT: A 505 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8142 (p90) REVERT: B 416 TYR cc_start: 0.8464 (p90) cc_final: 0.8173 (p90) outliers start: 35 outliers final: 22 residues processed: 104 average time/residue: 0.1505 time to fit residues: 22.6894 Evaluate side-chains 104 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR 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 335 LEU Chi-restraints excluded: chain B residue 381 ILE 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: 0.9980 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3817 r_free = 0.3817 target = 0.104896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083948 restraints weight = 19399.205| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 5.08 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.206 Angle : 0.655 11.831 9787 Z= 0.317 Chirality : 0.046 0.284 1050 Planarity : 0.004 0.043 1106 Dihedral : 18.609 143.997 1277 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 6.07 % Allowed : 25.64 % Favored : 68.29 % 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: -1.83 (0.30), residues: 732 helix: -0.77 (0.33), residues: 212 sheet: -1.28 (0.44), residues: 140 loop : -1.39 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.020 0.001 PHE B 305 TYR 0.020 0.001 TYR A 104 ARG 0.002 0.000 ARG B 283 *********************** 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 132 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6596 (pmm) cc_final: 0.6375 (pmm) REVERT: A 289 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 368 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8753 (pp20) REVERT: A 436 GLU cc_start: 0.6773 (mm-30) cc_final: 0.5862 (mm-30) REVERT: A 444 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 476 GLU cc_start: 0.8017 (pm20) cc_final: 0.7617 (pm20) REVERT: A 505 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.8049 (p90) REVERT: B 191 ASP cc_start: 0.8819 (t0) cc_final: 0.8557 (t0) REVERT: B 273 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: B 274 GLU cc_start: 0.8820 (mp0) cc_final: 0.8565 (mp0) REVERT: B 328 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8614 (mtmm) outliers start: 40 outliers final: 21 residues processed: 119 average time/residue: 0.1569 time to fit residues: 26.3330 Evaluate side-chains 111 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 273 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3834 r_free = 0.3834 target = 0.105810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084526 restraints weight = 19425.818| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 5.11 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 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 = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 0.049 7122 Z= 0.206 Angle : 0.654 12.807 9787 Z= 0.317 Chirality : 0.046 0.284 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.511 143.563 1277 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.86 % Allowed : 27.01 % Favored : 68.13 % 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: -0.63 (0.33), residues: 211 sheet: -1.35 (0.44), residues: 140 loop : -1.40 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 320 HIS 0.002 0.001 HIS B 320 PHE 0.018 0.001 PHE B 305 TYR 0.021 0.001 TYR B 416 ARG 0.004 0.000 ARG B 250 *********************** 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 119 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6598 (pmm) cc_final: 0.6361 (pmm) REVERT: A 289 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: A 368 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8708 (pp20) REVERT: A 436 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6035 (mm-30) REVERT: A 444 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 476 GLU cc_start: 0.8042 (pm20) cc_final: 0.7626 (pm20) REVERT: A 505 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.8085 (p90) REVERT: B 273 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: B 274 GLU cc_start: 0.8842 (mp0) cc_final: 0.8558 (mp0) REVERT: B 328 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8522 (mtmm) REVERT: B 336 MET cc_start: 0.7521 (tpp) cc_final: 0.7233 (mpp) outliers start: 32 outliers final: 22 residues processed: 108 average time/residue: 0.1554 time to fit residues: 24.4693 Evaluate side-chains 113 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 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 273 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3850 r_free = 0.3850 target = 0.106535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085875 restraints weight = 19260.817| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.01 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 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 = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.214 Angle : 0.659 13.577 9787 Z= 0.317 Chirality : 0.046 0.284 1050 Planarity : 0.004 0.040 1106 Dihedral : 18.467 143.163 1277 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.61 % Allowed : 28.38 % Favored : 66.01 % 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: -1.75 (0.30), residues: 732 helix: -0.58 (0.33), residues: 213 sheet: -1.41 (0.44), residues: 140 loop : -1.34 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 320 HIS 0.002 0.000 HIS B 320 PHE 0.017 0.001 PHE B 411 TYR 0.019 0.001 TYR A 104 ARG 0.002 0.000 ARG B 250 *********************** 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 124 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6606 (pmm) cc_final: 0.6370 (pmm) REVERT: A 213 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: A 289 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: A 330 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 368 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8710 (pp20) REVERT: A 436 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6254 (mm-30) REVERT: A 444 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 476 GLU cc_start: 0.8070 (pm20) cc_final: 0.7610 (pm20) REVERT: A 505 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8065 (p90) REVERT: B 191 ASP cc_start: 0.8827 (t0) cc_final: 0.8562 (t0) REVERT: B 273 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 274 GLU cc_start: 0.8861 (mp0) cc_final: 0.8628 (mp0) REVERT: B 336 MET cc_start: 0.7406 (tpp) cc_final: 0.6800 (mmt) outliers start: 37 outliers final: 21 residues processed: 112 average time/residue: 0.1678 time to fit residues: 26.2781 Evaluate side-chains 110 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 122 ASN Chi-restraints excluded: chain A residue 124 LYS 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 330 LEU 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 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 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.105689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085038 restraints weight = 19172.448| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 5.01 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2280 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= 0.231 Angle : 0.659 13.488 9787 Z= 0.320 Chirality : 0.046 0.286 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.512 142.911 1277 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.16 % Allowed : 28.83 % Favored : 66.01 % 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: -0.53 (0.34), residues: 213 sheet: -1.35 (0.44), residues: 140 loop : -1.33 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 320 HIS 0.003 0.001 HIS B 320 PHE 0.018 0.001 PHE B 411 TYR 0.021 0.001 TYR B 416 ARG 0.002 0.000 ARG B 250 *********************** 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 115 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6558 (pmm) cc_final: 0.6346 (pmm) REVERT: A 263 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8131 (mmtt) REVERT: A 289 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: A 368 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8725 (pp20) REVERT: A 436 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6546 (mm-30) REVERT: A 444 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 476 GLU cc_start: 0.8118 (pm20) cc_final: 0.7639 (pm20) REVERT: A 505 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.8038 (p90) REVERT: B 273 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: B 274 GLU cc_start: 0.8868 (mp0) cc_final: 0.8647 (mp0) outliers start: 34 outliers final: 20 residues processed: 105 average time/residue: 0.1489 time to fit residues: 22.4464 Evaluate side-chains 106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 295 GLN Chi-restraints excluded: chain A residue 338 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 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 273 PHE Chi-restraints excluded: chain B residue 277 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3860 r_free = 0.3860 target = 0.107249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085787 restraints weight = 19480.282| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.28 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 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 = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7122 Z= 0.208 Angle : 0.663 13.368 9787 Z= 0.321 Chirality : 0.046 0.293 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.530 142.386 1277 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.10 % Allowed : 30.05 % Favored : 65.86 % 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: -0.48 (0.34), residues: 211 sheet: -1.33 (0.44), residues: 140 loop : -1.30 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 320 HIS 0.003 0.001 HIS A 329 PHE 0.024 0.001 PHE B 411 TYR 0.024 0.001 TYR A 56 ARG 0.001 0.000 ARG B 283 *********************** 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 106 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6595 (pmm) cc_final: 0.6361 (pmm) REVERT: A 102 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7754 (tpm170) REVERT: A 263 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8019 (mmtt) REVERT: A 289 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 368 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8713 (pp20) REVERT: A 436 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6583 (mm-30) REVERT: A 444 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 476 GLU cc_start: 0.8112 (pm20) cc_final: 0.7631 (pm20) REVERT: A 505 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.8034 (p90) REVERT: B 262 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: B 273 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8226 (m-80) outliers start: 27 outliers final: 18 residues processed: 97 average time/residue: 0.1722 time to fit residues: 23.3649 Evaluate side-chains 101 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 121 PHE 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 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 368 GLU 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 273 PHE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 345 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.106993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085986 restraints weight = 19592.029| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 5.19 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7122 Z= 0.179 Angle : 0.659 13.527 9787 Z= 0.319 Chirality : 0.046 0.305 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.529 141.476 1277 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.34 % Allowed : 30.96 % 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: -1.58 (0.30), residues: 732 helix: -0.44 (0.34), residues: 211 sheet: -1.07 (0.45), residues: 133 loop : -1.34 (0.31), residues: 388 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 0.012 0.001 PHE B 273 TYR 0.019 0.001 TYR B 416 ARG 0.003 0.000 ARG B 283 *********************** 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 108 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.9515 (mm-30) cc_final: 0.8812 (pp20) REVERT: A 289 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 436 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 444 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 476 GLU cc_start: 0.8142 (pm20) cc_final: 0.7711 (pm20) REVERT: B 262 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: B 273 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: B 336 MET cc_start: 0.7647 (tpp) cc_final: 0.7286 (mmm) outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.1446 time to fit residues: 21.5574 Evaluate side-chains 99 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 124 LYS Chi-restraints excluded: chain A residue 219 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 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 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 411 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3852 r_free = 0.3852 target = 0.106926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085618 restraints weight = 19828.189| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 5.26 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7122 Z= 0.197 Angle : 0.667 14.842 9787 Z= 0.320 Chirality : 0.046 0.297 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.552 141.542 1277 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.58 % Allowed : 31.41 % Favored : 66.01 % 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: -0.41 (0.34), residues: 209 sheet: -1.00 (0.46), residues: 133 loop : -1.33 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 320 HIS 0.002 0.001 HIS B 320 PHE 0.015 0.001 PHE B 411 TYR 0.028 0.001 TYR A 56 ARG 0.001 0.000 ARG B 283 ********************** 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 97 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.9502 (mm-30) cc_final: 0.8799 (pp20) REVERT: A 263 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8027 (mmtt) REVERT: A 289 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: A 436 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 444 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 476 GLU cc_start: 0.8140 (pm20) cc_final: 0.7701 (pm20) REVERT: B 273 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8330 (m-80) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1478 time to fit residues: 19.4814 Evaluate side-chains 95 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 124 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 252 LEU 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 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 381 ILE 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: 2.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3821 r_free = 0.3821 target = 0.105572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083931 restraints weight = 19678.574| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 5.29 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7122 Z= 0.217 Angle : 0.663 14.693 9787 Z= 0.320 Chirality : 0.046 0.295 1050 Planarity : 0.004 0.041 1106 Dihedral : 18.563 141.946 1277 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.34 % Allowed : 30.65 % Favored : 66.01 % 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: -0.41 (0.34), residues: 209 sheet: -0.98 (0.46), residues: 133 loop : -1.33 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 320 HIS 0.002 0.000 HIS A 207 PHE 0.016 0.001 PHE B 411 TYR 0.020 0.001 TYR B 416 ARG 0.002 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2767.13 seconds wall clock time: 48 minutes 32.72 seconds (2912.72 seconds total)