Starting phenix.real_space_refine on Sat Apr 6 09:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9g_36095/04_2024/8j9g_36095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9g_36095/04_2024/8j9g_36095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9g_36095/04_2024/8j9g_36095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9g_36095/04_2024/8j9g_36095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9g_36095/04_2024/8j9g_36095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9g_36095/04_2024/8j9g_36095.pdb" } resolution = 3.5 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= 0.014 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 24 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 5006 2.51 5 N 1318 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 301": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7868 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3759 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "E" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 9, 'RNA': 3} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 246 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} 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: 4.74, per 1000 atoms: 0.60 Number of scatterers: 7868 At special positions: 0 Unit cell: (91.35, 92.4, 131.25, 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 22 16.00 P 24 15.00 Mg 1 11.99 O 1497 8.00 N 1318 7.00 C 5006 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 - 3.50 Amino acid : False - 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 33.4% alpha, 13.4% beta 6 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 2.80 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 30 Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.592A pdb=" N ASP A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 109 through 132 removed outlier: 4.305A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.883A pdb=" N GLU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.501A pdb=" N ALA A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.679A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.792A pdb=" N LYS A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.953A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 29 removed outlier: 4.188A pdb=" N TRP B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 4.517A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 123 through 138 removed outlier: 4.049A pdb=" N GLY B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.539A pdb=" N PHE B 158 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.922A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.738A pdb=" N LEU B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 257 through 272 removed outlier: 3.630A pdb=" N CYS B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.820A pdb=" N ARG B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.827A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.720A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.132A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 450 removed outlier: 4.240A pdb=" N GLU B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.912A pdb=" N LYS A 2 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS B 413 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 169 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B 414 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS B 167 " --> pdb=" O MET B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 7.007A pdb=" N GLY A 385 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.668A pdb=" N GLN A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.694A pdb=" N PHE A 140 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 142 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.523A pdb=" N VAL A 284 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 300 " --> pdb=" O VAL A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.717A pdb=" N GLY A 318 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.188A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.500A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.500A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 328 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 179 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 187 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.597A pdb=" N ILE B 208 " --> pdb=" O CYS B 215 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2266 1.34 - 1.45: 1396 1.45 - 1.57: 4365 1.57 - 1.69: 46 1.69 - 1.81: 34 Bond restraints: 8107 Sorted by residual: bond pdb=" C MET B 345 " pdb=" N ASP B 346 " ideal model delta sigma weight residual 1.332 1.315 0.018 1.40e-02 5.10e+03 1.61e+00 bond pdb=" CA TYR A 505 " pdb=" C TYR A 505 " ideal model delta sigma weight residual 1.523 1.502 0.022 1.80e-02 3.09e+03 1.44e+00 bond pdb=" C3' C E 7 " pdb=" O3' C E 7 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.36e-01 bond pdb=" C3' DA F 16 " pdb=" O3' DA F 16 " ideal model delta sigma weight residual 1.422 1.446 -0.024 3.00e-02 1.11e+03 6.47e-01 bond pdb=" C TYR A 505 " pdb=" O TYR A 505 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.47e-02 4.63e+03 5.74e-01 ... (remaining 8102 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.84: 268 105.84 - 112.89: 4310 112.89 - 119.94: 2781 119.94 - 127.00: 3547 127.00 - 134.05: 149 Bond angle restraints: 11055 Sorted by residual: angle pdb=" N TYR A 505 " pdb=" CA TYR A 505 " pdb=" C TYR A 505 " ideal model delta sigma weight residual 113.15 107.99 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" N PRO A 499 " pdb=" CA PRO A 499 " pdb=" C PRO A 499 " ideal model delta sigma weight residual 110.70 114.11 -3.41 1.22e+00 6.72e-01 7.82e+00 angle pdb=" C VAL A 92 " pdb=" N PHE A 93 " pdb=" CA PHE A 93 " ideal model delta sigma weight residual 122.46 125.98 -3.52 1.41e+00 5.03e-01 6.24e+00 angle pdb=" CA LEU A 462 " pdb=" CB LEU A 462 " pdb=" CG LEU A 462 " ideal model delta sigma weight residual 116.30 124.35 -8.05 3.50e+00 8.16e-02 5.29e+00 angle pdb=" CA LYS A 447 " pdb=" CB LYS A 447 " pdb=" CG LYS A 447 " ideal model delta sigma weight residual 114.10 118.59 -4.49 2.00e+00 2.50e-01 5.03e+00 ... (remaining 11050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 4383 27.74 - 55.48: 395 55.48 - 83.22: 36 83.22 - 110.96: 4 110.96 - 138.70: 2 Dihedral angle restraints: 4820 sinusoidal: 2180 harmonic: 2640 Sorted by residual: dihedral pdb=" CA ARG A 225 " pdb=" C ARG A 225 " pdb=" N GLU A 226 " pdb=" CA GLU A 226 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA PRO A 499 " pdb=" C PRO A 499 " pdb=" N PRO A 500 " pdb=" CA PRO A 500 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+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 81.30 138.70 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 4817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 937 0.046 - 0.092: 199 0.092 - 0.138: 55 0.138 - 0.184: 1 0.184 - 0.229: 2 Chirality restraints: 1194 Sorted by residual: 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 2.23 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" P U E 1 " pdb=" OP1 U E 1 " pdb=" OP2 U E 1 " pdb=" O5' U E 1 " both_signs ideal model delta sigma weight residual True 2.17 2.37 -0.20 2.00e-01 2.50e+01 9.79e-01 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 2.51 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1191 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 499 " 0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 500 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 498 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 499 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 112 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C ILE B 112 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE B 112 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL B 113 " -0.008 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 108 2.58 - 3.16: 6585 3.16 - 3.74: 13629 3.74 - 4.32: 17402 4.32 - 4.90: 27712 Nonbonded interactions: 65436 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG A 601 " model vdw 1.995 2.170 nonbonded pdb=" OD1 ASN A 468 " pdb="MG MG A 601 " model vdw 2.025 2.170 nonbonded pdb=" ND2 ASN A 468 " pdb="MG MG A 601 " model vdw 2.121 2.250 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.153 2.440 nonbonded pdb=" OG SER B 385 " pdb=" O ASP B 387 " model vdw 2.183 2.440 ... (remaining 65431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.68 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 : 0.003 0.037 8107 Z= 0.162 Angle : 0.517 8.050 11055 Z= 0.274 Chirality : 0.041 0.229 1194 Planarity : 0.004 0.088 1322 Dihedral : 19.064 138.697 3112 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.25 % Allowed : 29.98 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.28), residues: 892 helix: 0.55 (0.34), residues: 239 sheet: -0.98 (0.43), residues: 154 loop : -1.78 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.003 0.001 HIS A 251 PHE 0.013 0.001 PHE A 93 TYR 0.021 0.001 TYR B 416 ARG 0.004 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 321 TYR cc_start: 0.6264 (t80) cc_final: 0.5770 (t80) REVERT: A 435 MET cc_start: 0.8705 (mmm) cc_final: 0.8035 (mmt) REVERT: A 474 ASP cc_start: 0.5790 (t0) cc_final: 0.5276 (t0) REVERT: B 1 MET cc_start: 0.6309 (pmm) cc_final: 0.6010 (ptm) REVERT: B 14 ASP cc_start: 0.8357 (p0) cc_final: 0.8134 (p0) REVERT: B 88 LEU cc_start: 0.8882 (tp) cc_final: 0.8657 (tp) REVERT: B 92 MET cc_start: 0.8537 (mmp) cc_final: 0.8274 (mmp) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.2554 time to fit residues: 39.0066 Evaluate side-chains 92 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.0170 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 147 HIS B 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8107 Z= 0.199 Angle : 0.598 8.876 11055 Z= 0.316 Chirality : 0.045 0.233 1194 Planarity : 0.005 0.088 1322 Dihedral : 15.769 146.243 1243 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.61 % Allowed : 31.09 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 892 helix: 0.58 (0.31), residues: 260 sheet: -0.85 (0.43), residues: 139 loop : -2.03 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.004 0.001 HIS B 340 PHE 0.025 0.002 PHE A 93 TYR 0.017 0.001 TYR B 416 ARG 0.006 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7821 (mmmm) REVERT: A 302 GLN cc_start: 0.6945 (tt0) cc_final: 0.6476 (mt0) REVERT: A 321 TYR cc_start: 0.5851 (t80) cc_final: 0.5456 (t80) REVERT: A 435 MET cc_start: 0.8586 (mmm) cc_final: 0.7944 (mmt) REVERT: A 507 ILE cc_start: 0.7838 (tt) cc_final: 0.7588 (tt) REVERT: B 1 MET cc_start: 0.6254 (pmm) cc_final: 0.6049 (ptm) REVERT: B 14 ASP cc_start: 0.8364 (p0) cc_final: 0.8138 (p0) REVERT: B 88 LEU cc_start: 0.8996 (tp) cc_final: 0.8729 (tt) REVERT: B 92 MET cc_start: 0.8516 (mmp) cc_final: 0.8269 (mmp) REVERT: B 285 TYR cc_start: 0.8043 (t80) cc_final: 0.7790 (t80) outliers start: 29 outliers final: 15 residues processed: 134 average time/residue: 0.2174 time to fit residues: 39.0577 Evaluate side-chains 118 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8107 Z= 0.204 Angle : 0.586 8.931 11055 Z= 0.307 Chirality : 0.044 0.229 1194 Planarity : 0.004 0.089 1322 Dihedral : 15.753 147.319 1243 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.73 % Allowed : 32.71 % Favored : 63.56 % 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: -1.41 (0.28), residues: 892 helix: 0.78 (0.31), residues: 261 sheet: -0.79 (0.43), residues: 139 loop : -2.02 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 368 HIS 0.004 0.001 HIS B 340 PHE 0.022 0.002 PHE A 93 TYR 0.015 0.001 TYR B 416 ARG 0.005 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.7947 (pt0) cc_final: 0.7682 (pm20) REVERT: A 287 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7844 (mmmt) REVERT: A 302 GLN cc_start: 0.7121 (tt0) cc_final: 0.6770 (mt0) REVERT: A 321 TYR cc_start: 0.5806 (t80) cc_final: 0.5373 (t80) REVERT: A 350 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8296 (t0) REVERT: A 435 MET cc_start: 0.8604 (mmm) cc_final: 0.7936 (mmt) REVERT: A 482 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: B 14 ASP cc_start: 0.8387 (p0) cc_final: 0.8134 (p0) REVERT: B 88 LEU cc_start: 0.9006 (tp) cc_final: 0.8754 (tt) REVERT: B 92 MET cc_start: 0.8585 (mmp) cc_final: 0.8345 (mmp) outliers start: 30 outliers final: 16 residues processed: 133 average time/residue: 0.2312 time to fit residues: 41.1495 Evaluate side-chains 116 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 0.0470 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.0670 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8107 Z= 0.177 Angle : 0.584 9.704 11055 Z= 0.303 Chirality : 0.044 0.222 1194 Planarity : 0.004 0.088 1322 Dihedral : 15.735 147.088 1243 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.10 % Allowed : 32.46 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.28), residues: 892 helix: 0.77 (0.31), residues: 267 sheet: -0.67 (0.43), residues: 144 loop : -2.08 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 368 HIS 0.003 0.001 HIS B 340 PHE 0.020 0.001 PHE A 93 TYR 0.014 0.001 TYR B 416 ARG 0.004 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7418 (mm) REVERT: A 287 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8067 (mmmt) REVERT: A 302 GLN cc_start: 0.7267 (tt0) cc_final: 0.6871 (mt0) REVERT: A 321 TYR cc_start: 0.5837 (t80) cc_final: 0.5484 (t80) REVERT: A 350 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8555 (t0) REVERT: A 406 MET cc_start: 0.7742 (pmm) cc_final: 0.7338 (pmm) REVERT: A 435 MET cc_start: 0.8527 (mmm) cc_final: 0.7913 (mmt) REVERT: A 482 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: B 14 ASP cc_start: 0.8359 (p0) cc_final: 0.8119 (p0) REVERT: B 55 GLU cc_start: 0.5727 (tm-30) cc_final: 0.5517 (tm-30) REVERT: B 92 MET cc_start: 0.8566 (mmp) cc_final: 0.8326 (mmp) outliers start: 33 outliers final: 16 residues processed: 139 average time/residue: 0.2207 time to fit residues: 41.2619 Evaluate side-chains 115 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8107 Z= 0.324 Angle : 0.659 9.025 11055 Z= 0.344 Chirality : 0.047 0.250 1194 Planarity : 0.005 0.092 1322 Dihedral : 15.991 146.598 1243 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.09 % Allowed : 30.97 % Favored : 62.94 % 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 (0.28), residues: 892 helix: 0.81 (0.32), residues: 254 sheet: -0.98 (0.41), residues: 147 loop : -2.12 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 368 HIS 0.006 0.001 HIS B 147 PHE 0.026 0.002 PHE A 93 TYR 0.014 0.002 TYR B 416 ARG 0.007 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7338 (mm) REVERT: A 302 GLN cc_start: 0.7349 (tt0) cc_final: 0.7060 (mt0) REVERT: A 321 TYR cc_start: 0.5919 (t80) cc_final: 0.5614 (t80) REVERT: A 350 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8734 (t0) REVERT: A 406 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6823 (pmm) REVERT: A 435 MET cc_start: 0.8622 (mmm) cc_final: 0.8029 (mmt) REVERT: A 482 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: B 14 ASP cc_start: 0.8373 (p0) cc_final: 0.8134 (p0) REVERT: B 92 MET cc_start: 0.8642 (mmp) cc_final: 0.8396 (mmp) REVERT: B 290 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7923 (p) outliers start: 49 outliers final: 31 residues processed: 147 average time/residue: 0.2201 time to fit residues: 43.6356 Evaluate side-chains 134 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8107 Z= 0.203 Angle : 0.635 9.932 11055 Z= 0.321 Chirality : 0.046 0.311 1194 Planarity : 0.004 0.088 1322 Dihedral : 15.957 148.542 1243 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.48 % Allowed : 32.34 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.28), residues: 892 helix: 0.78 (0.32), residues: 266 sheet: -0.78 (0.42), residues: 146 loop : -2.17 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 373 HIS 0.004 0.001 HIS B 340 PHE 0.021 0.001 PHE A 93 TYR 0.014 0.001 TYR B 416 ARG 0.004 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 113 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7458 (mm) REVERT: A 287 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8383 (mmmt) REVERT: A 302 GLN cc_start: 0.7385 (tt0) cc_final: 0.6979 (mt0) REVERT: A 321 TYR cc_start: 0.5837 (t80) cc_final: 0.5564 (t80) REVERT: A 350 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8819 (t0) REVERT: A 406 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6825 (pmm) REVERT: A 435 MET cc_start: 0.8540 (mmm) cc_final: 0.8006 (mmt) REVERT: A 482 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: A 505 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: B 1 MET cc_start: 0.6955 (ptm) cc_final: 0.6472 (ptt) REVERT: B 55 GLU cc_start: 0.5798 (tm-30) cc_final: 0.5112 (tm-30) REVERT: B 92 MET cc_start: 0.8624 (mmp) cc_final: 0.8387 (mmp) REVERT: B 290 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7877 (p) outliers start: 36 outliers final: 23 residues processed: 143 average time/residue: 0.2263 time to fit residues: 43.1421 Evaluate side-chains 133 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8107 Z= 0.206 Angle : 0.638 9.956 11055 Z= 0.326 Chirality : 0.045 0.230 1194 Planarity : 0.004 0.086 1322 Dihedral : 15.949 148.758 1243 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.98 % Allowed : 32.46 % Favored : 62.56 % 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: -1.40 (0.28), residues: 892 helix: 0.86 (0.33), residues: 261 sheet: -0.75 (0.42), residues: 146 loop : -2.10 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 373 HIS 0.010 0.001 HIS A 67 PHE 0.019 0.001 PHE A 93 TYR 0.030 0.001 TYR B 416 ARG 0.005 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7485 (mm) REVERT: A 302 GLN cc_start: 0.7415 (tt0) cc_final: 0.7109 (mt0) REVERT: A 321 TYR cc_start: 0.5858 (t80) cc_final: 0.5617 (t80) REVERT: A 406 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6802 (pmm) REVERT: A 435 MET cc_start: 0.8495 (mmm) cc_final: 0.7921 (mmt) REVERT: A 505 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: B 1 MET cc_start: 0.7031 (ptm) cc_final: 0.6555 (ptt) REVERT: B 55 GLU cc_start: 0.5684 (tm-30) cc_final: 0.5008 (tm-30) REVERT: B 92 MET cc_start: 0.8619 (mmp) cc_final: 0.8376 (mmp) REVERT: B 364 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7984 (tp-100) outliers start: 40 outliers final: 32 residues processed: 137 average time/residue: 0.2449 time to fit residues: 44.9673 Evaluate side-chains 136 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8107 Z= 0.311 Angle : 0.682 9.507 11055 Z= 0.354 Chirality : 0.047 0.251 1194 Planarity : 0.005 0.086 1322 Dihedral : 16.169 148.575 1243 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.85 % Allowed : 30.97 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.28), residues: 892 helix: 0.90 (0.33), residues: 251 sheet: -0.70 (0.43), residues: 131 loop : -2.09 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 373 HIS 0.007 0.001 HIS A 67 PHE 0.024 0.002 PHE A 93 TYR 0.028 0.002 TYR B 416 ARG 0.006 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 107 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 302 GLN cc_start: 0.7446 (tt0) cc_final: 0.7137 (mt0) REVERT: A 321 TYR cc_start: 0.5918 (t80) cc_final: 0.5704 (t80) REVERT: A 350 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8565 (t0) REVERT: A 406 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6879 (pmm) REVERT: A 435 MET cc_start: 0.8584 (mmm) cc_final: 0.8047 (mmt) REVERT: A 505 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: B 1 MET cc_start: 0.7147 (ptm) cc_final: 0.6580 (ptt) REVERT: B 55 GLU cc_start: 0.5807 (tm-30) cc_final: 0.5075 (tm-30) REVERT: B 92 MET cc_start: 0.8693 (mmp) cc_final: 0.8458 (mmp) outliers start: 47 outliers final: 37 residues processed: 143 average time/residue: 0.2127 time to fit residues: 40.7685 Evaluate side-chains 142 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8107 Z= 0.179 Angle : 0.648 10.423 11055 Z= 0.329 Chirality : 0.045 0.223 1194 Planarity : 0.004 0.082 1322 Dihedral : 16.057 150.765 1243 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.98 % Allowed : 31.72 % Favored : 63.31 % 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: -1.40 (0.28), residues: 892 helix: 0.75 (0.32), residues: 266 sheet: -0.62 (0.43), residues: 148 loop : -2.11 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 373 HIS 0.004 0.001 HIS A 67 PHE 0.020 0.001 PHE A 93 TYR 0.028 0.001 TYR B 416 ARG 0.007 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7476 (mm) REVERT: A 302 GLN cc_start: 0.7401 (tt0) cc_final: 0.7002 (mt0) REVERT: A 349 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: A 350 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8571 (t0) REVERT: A 406 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6820 (pmm) REVERT: A 435 MET cc_start: 0.8455 (mmm) cc_final: 0.7870 (mmt) REVERT: A 481 ARG cc_start: 0.6530 (ttm170) cc_final: 0.6287 (mtp180) REVERT: B 1 MET cc_start: 0.7243 (ptm) cc_final: 0.6691 (ptt) REVERT: B 55 GLU cc_start: 0.5659 (tm-30) cc_final: 0.4949 (tm-30) REVERT: B 92 MET cc_start: 0.8677 (mmp) cc_final: 0.8435 (mmp) REVERT: B 364 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8095 (tp-100) outliers start: 40 outliers final: 29 residues processed: 143 average time/residue: 0.2327 time to fit residues: 44.3506 Evaluate side-chains 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8107 Z= 0.189 Angle : 0.651 10.399 11055 Z= 0.332 Chirality : 0.045 0.221 1194 Planarity : 0.004 0.084 1322 Dihedral : 15.899 150.829 1243 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.98 % Allowed : 31.84 % Favored : 64.18 % 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: -1.34 (0.28), residues: 892 helix: 0.86 (0.32), residues: 265 sheet: -0.58 (0.42), residues: 146 loop : -2.09 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 373 HIS 0.004 0.001 HIS A 67 PHE 0.020 0.002 PHE A 93 TYR 0.028 0.002 TYR B 416 ARG 0.006 0.001 ARG A 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7488 (mm) REVERT: A 302 GLN cc_start: 0.7370 (tt0) cc_final: 0.7082 (mt0) REVERT: A 350 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8444 (t0) REVERT: A 371 ASN cc_start: 0.8220 (m110) cc_final: 0.7864 (m110) REVERT: A 406 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6792 (pmm) REVERT: B 92 MET cc_start: 0.8676 (mmp) cc_final: 0.8435 (mmp) REVERT: B 364 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8083 (tp-100) outliers start: 32 outliers final: 29 residues processed: 130 average time/residue: 0.2285 time to fit residues: 39.6864 Evaluate side-chains 135 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096929 restraints weight = 25681.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.099623 restraints weight = 13918.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.101425 restraints weight = 9250.001| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8107 Z= 0.185 Angle : 0.655 10.206 11055 Z= 0.333 Chirality : 0.045 0.219 1194 Planarity : 0.004 0.084 1322 Dihedral : 15.747 150.999 1243 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.73 % Allowed : 33.21 % Favored : 63.06 % 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: -1.28 (0.28), residues: 892 helix: 0.96 (0.33), residues: 259 sheet: -0.70 (0.42), residues: 148 loop : -2.00 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 373 HIS 0.003 0.001 HIS A 67 PHE 0.020 0.002 PHE A 93 TYR 0.027 0.001 TYR B 416 ARG 0.006 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.23 seconds wall clock time: 36 minutes 47.98 seconds (2207.98 seconds total)