Starting phenix.real_space_refine on Fri Dec 27 14:00:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vu8_21388/12_2024/6vu8_21388.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vu8_21388/12_2024/6vu8_21388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vu8_21388/12_2024/6vu8_21388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vu8_21388/12_2024/6vu8_21388.map" model { file = "/net/cci-nas-00/data/ceres_data/6vu8_21388/12_2024/6vu8_21388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vu8_21388/12_2024/6vu8_21388.cif" } resolution = 4.14 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= 0.005 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 3313 2.51 5 N 913 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5249 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3815 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 461} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1434 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 3.46, per 1000 atoms: 0.66 Number of scatterers: 5249 At special positions: 0 Unit cell: (118.72, 64.66, 87.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 991 8.00 N 913 7.00 C 3313 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: 1.40 Conformation dependent library (CDL) restraints added in 599.7 milliseconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1278 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 56.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.592A pdb=" N VAL A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 29 removed outlier: 4.233A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 57 Processing helix chain 'A' and resid 62 through 75 removed outlier: 4.125A pdb=" N TRP A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.700A pdb=" N LEU A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.806A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 removed outlier: 3.517A pdb=" N GLN A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.706A pdb=" N GLN A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 4.282A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.782A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 260 removed outlier: 4.609A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 260 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.884A pdb=" N HIS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.161A pdb=" N LEU A 292 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 321 removed outlier: 4.539A pdb=" N HIS A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 344 through 356 removed outlier: 4.481A pdb=" N ARG A 348 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A 350 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.886A pdb=" N ARG A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.839A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 6.388A pdb=" N GLY A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 4.288A pdb=" N LEU A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.543A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.584A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.605A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.026A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.554A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 351 removed outlier: 4.332A pdb=" N THR B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 220 through 225 removed outlier: 3.588A pdb=" N ALA B 220 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 265 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N CYS B 224 " --> pdb=" O PHE B 267 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1770 1.34 - 1.46: 1040 1.46 - 1.58: 2479 1.58 - 1.70: 7 1.70 - 1.81: 44 Bond restraints: 5340 Sorted by residual: bond pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.525 1.608 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O3P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C ALA A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.337 1.374 -0.036 1.24e-02 6.50e+03 8.64e+00 bond pdb=" O2P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.481 0.047 2.00e-02 2.50e+03 5.51e+00 ... (remaining 5335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 7033 2.77 - 5.54: 161 5.54 - 8.31: 23 8.31 - 11.08: 8 11.08 - 13.85: 3 Bond angle restraints: 7228 Sorted by residual: angle pdb=" C GLN A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" N SER A 30 " pdb=" CA SER A 30 " pdb=" C SER A 30 " ideal model delta sigma weight residual 110.97 115.96 -4.99 1.09e+00 8.42e-01 2.09e+01 angle pdb=" C ARG B 313 " pdb=" N LYS B 314 " pdb=" CA LYS B 314 " ideal model delta sigma weight residual 122.61 129.06 -6.45 1.56e+00 4.11e-01 1.71e+01 angle pdb=" C VAL B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 120.82 126.64 -5.82 1.41e+00 5.03e-01 1.70e+01 angle pdb=" CA LEU A 424 " pdb=" CB LEU A 424 " pdb=" CG LEU A 424 " ideal model delta sigma weight residual 116.30 130.15 -13.85 3.50e+00 8.16e-02 1.56e+01 ... (remaining 7223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2835 17.89 - 35.78: 355 35.78 - 53.67: 54 53.67 - 71.55: 11 71.55 - 89.44: 9 Dihedral angle restraints: 3264 sinusoidal: 1306 harmonic: 1958 Sorted by residual: dihedral pdb=" CA ASN A 207 " pdb=" C ASN A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ARG A 365 " pdb=" C ARG A 365 " pdb=" N PRO A 366 " pdb=" CA PRO A 366 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA B 41 " pdb=" C ALA B 41 " pdb=" N GLY B 42 " pdb=" CA GLY B 42 " ideal model delta harmonic sigma weight residual 180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 675 0.067 - 0.134: 137 0.134 - 0.202: 16 0.202 - 0.269: 2 0.269 - 0.336: 1 Chirality restraints: 831 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CG LEU A 418 " pdb=" CB LEU A 418 " pdb=" CD1 LEU A 418 " pdb=" CD2 LEU A 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 377 " pdb=" CA VAL A 377 " pdb=" CG1 VAL A 377 " pdb=" CG2 VAL A 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 828 not shown) Planarity restraints: 939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 365 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO A 366 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 287 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 288 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 203 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 204 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.035 5.00e-02 4.00e+02 ... (remaining 936 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1322 2.79 - 3.32: 5039 3.32 - 3.84: 8432 3.84 - 4.37: 9418 4.37 - 4.90: 15249 Nonbonded interactions: 39460 Sorted by model distance: nonbonded pdb=" O PHE A 270 " pdb=" OG1 THR A 274 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU A 197 " pdb=" OH TYR A 249 " model vdw 2.313 3.040 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 260 " model vdw 2.317 3.040 nonbonded pdb=" O PHE A 406 " pdb=" OG1 THR A 410 " model vdw 2.326 3.040 nonbonded pdb=" NH2 ARG A 255 " pdb=" O LEU A 286 " model vdw 2.334 3.120 ... (remaining 39455 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.006 0.104 5340 Z= 0.386 Angle : 1.053 13.846 7228 Z= 0.553 Chirality : 0.054 0.336 831 Planarity : 0.007 0.065 939 Dihedral : 16.207 89.443 1986 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.24), residues: 655 helix: -2.78 (0.20), residues: 332 sheet: -3.68 (0.93), residues: 21 loop : -3.80 (0.29), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 66 HIS 0.004 0.001 HIS A 477 PHE 0.015 0.002 PHE A 232 TYR 0.015 0.003 TYR A 445 ARG 0.009 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8585 (p0) cc_final: 0.8345 (p0) REVERT: A 27 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8624 (ttp-110) REVERT: A 66 TRP cc_start: 0.8568 (m-90) cc_final: 0.8303 (m-90) REVERT: A 97 ASP cc_start: 0.9469 (t70) cc_final: 0.9202 (t0) REVERT: A 151 TYR cc_start: 0.8069 (p90) cc_final: 0.7860 (p90) REVERT: A 162 PHE cc_start: 0.9119 (t80) cc_final: 0.8542 (t80) REVERT: A 169 PHE cc_start: 0.8987 (t80) cc_final: 0.8728 (t80) REVERT: A 194 ASP cc_start: 0.9081 (m-30) cc_final: 0.8442 (m-30) REVERT: A 197 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8405 (mp0) REVERT: A 222 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 233 ASP cc_start: 0.8003 (p0) cc_final: 0.7739 (p0) REVERT: A 247 TYR cc_start: 0.8494 (m-80) cc_final: 0.8160 (m-80) REVERT: A 259 MET cc_start: 0.8229 (mmt) cc_final: 0.7968 (mmp) REVERT: A 328 GLU cc_start: 0.8336 (pt0) cc_final: 0.7983 (pt0) REVERT: A 352 LYS cc_start: 0.8627 (tptp) cc_final: 0.8418 (tptp) REVERT: A 356 LEU cc_start: 0.8773 (mp) cc_final: 0.7719 (mp) REVERT: B 205 ARG cc_start: 0.7434 (mmm160) cc_final: 0.6504 (mmt180) REVERT: B 241 ASN cc_start: 0.8572 (p0) cc_final: 0.7384 (p0) REVERT: B 242 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8375 (mtp180) REVERT: B 243 MET cc_start: 0.8217 (ppp) cc_final: 0.7900 (tmm) REVERT: B 244 HIS cc_start: 0.8743 (m-70) cc_final: 0.8320 (m-70) REVERT: B 247 MET cc_start: 0.8695 (mtt) cc_final: 0.8228 (mtt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1888 time to fit residues: 42.3777 Evaluate side-chains 136 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 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 29 HIS A 40 GLN A 87 GLN A 90 HIS A 229 ASN A 276 ASN A 344 HIS B 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5340 Z= 0.192 Angle : 0.675 8.333 7228 Z= 0.350 Chirality : 0.041 0.155 831 Planarity : 0.005 0.057 939 Dihedral : 6.192 25.342 730 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.36 % Allowed : 6.49 % Favored : 93.15 % 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: -3.30 (0.29), residues: 655 helix: -1.04 (0.26), residues: 341 sheet: -3.67 (0.86), residues: 21 loop : -3.56 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 258 HIS 0.006 0.001 HIS A 344 PHE 0.014 0.002 PHE A 163 TYR 0.015 0.002 TYR A 151 ARG 0.006 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7385 (mp0) cc_final: 0.7159 (pm20) REVERT: A 16 ASP cc_start: 0.8585 (p0) cc_final: 0.8339 (p0) REVERT: A 27 ARG cc_start: 0.8911 (ptm160) cc_final: 0.8662 (ptp90) REVERT: A 66 TRP cc_start: 0.8599 (m-90) cc_final: 0.8364 (m-90) REVERT: A 90 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8309 (t-90) REVERT: A 97 ASP cc_start: 0.9470 (t70) cc_final: 0.9086 (t0) REVERT: A 151 TYR cc_start: 0.7209 (p90) cc_final: 0.5605 (p90) REVERT: A 163 PHE cc_start: 0.9211 (m-80) cc_final: 0.8995 (m-80) REVERT: A 191 LEU cc_start: 0.9047 (pp) cc_final: 0.8627 (pp) REVERT: A 194 ASP cc_start: 0.8972 (m-30) cc_final: 0.8646 (m-30) REVERT: A 197 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 221 MET cc_start: 0.8750 (tpt) cc_final: 0.8076 (tpt) REVERT: A 233 ASP cc_start: 0.7951 (p0) cc_final: 0.7680 (p0) REVERT: A 247 TYR cc_start: 0.8483 (m-80) cc_final: 0.8147 (m-10) REVERT: A 352 LYS cc_start: 0.8591 (tptp) cc_final: 0.8388 (tptp) REVERT: A 356 LEU cc_start: 0.9022 (mp) cc_final: 0.8193 (mp) REVERT: A 396 PHE cc_start: 0.8372 (t80) cc_final: 0.7985 (t80) REVERT: A 445 TYR cc_start: 0.8061 (t80) cc_final: 0.7837 (t80) REVERT: B 205 ARG cc_start: 0.7713 (mmm160) cc_final: 0.6460 (mmt180) REVERT: B 241 ASN cc_start: 0.8662 (p0) cc_final: 0.6851 (p0) REVERT: B 243 MET cc_start: 0.7984 (ppp) cc_final: 0.7752 (tmm) REVERT: B 244 HIS cc_start: 0.8830 (m-70) cc_final: 0.8275 (m-70) REVERT: B 247 MET cc_start: 0.8482 (mtt) cc_final: 0.8150 (mtt) REVERT: B 311 ASN cc_start: 0.7531 (t0) cc_final: 0.7272 (t0) REVERT: B 340 THR cc_start: 0.9476 (m) cc_final: 0.9061 (t) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.1563 time to fit residues: 37.0278 Evaluate side-chains 144 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.0010 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 324 HIS A 344 HIS B 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5340 Z= 0.169 Angle : 0.648 8.429 7228 Z= 0.329 Chirality : 0.040 0.196 831 Planarity : 0.005 0.068 939 Dihedral : 5.586 23.465 730 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.36 % Allowed : 4.68 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.31), residues: 655 helix: -0.34 (0.28), residues: 343 sheet: -3.45 (0.92), residues: 21 loop : -3.45 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 258 HIS 0.007 0.001 HIS A 90 PHE 0.012 0.001 PHE A 163 TYR 0.022 0.002 TYR A 151 ARG 0.006 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.7990 (p) cc_final: 0.7632 (p) REVERT: A 97 ASP cc_start: 0.9455 (t70) cc_final: 0.9160 (t0) REVERT: A 118 LEU cc_start: 0.9079 (mm) cc_final: 0.8849 (mm) REVERT: A 151 TYR cc_start: 0.7215 (p90) cc_final: 0.5803 (p90) REVERT: A 233 ASP cc_start: 0.7993 (p0) cc_final: 0.7729 (p0) REVERT: A 247 TYR cc_start: 0.8592 (m-80) cc_final: 0.8171 (m-80) REVERT: A 317 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 328 GLU cc_start: 0.8196 (pt0) cc_final: 0.7929 (pt0) REVERT: B 205 ARG cc_start: 0.7742 (mmm160) cc_final: 0.6634 (mmt180) REVERT: B 241 ASN cc_start: 0.8548 (p0) cc_final: 0.7376 (p0) REVERT: B 243 MET cc_start: 0.7959 (ppp) cc_final: 0.7702 (tmm) REVERT: B 244 HIS cc_start: 0.8590 (m-70) cc_final: 0.7936 (m-70) REVERT: B 247 MET cc_start: 0.8604 (mtt) cc_final: 0.8134 (mtt) REVERT: B 271 LYS cc_start: 0.8315 (tmtt) cc_final: 0.7855 (tmtt) REVERT: B 290 TYR cc_start: 0.8258 (t80) cc_final: 0.8039 (t80) REVERT: B 354 PHE cc_start: 0.6978 (p90) cc_final: 0.6506 (p90) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.1692 time to fit residues: 40.7463 Evaluate side-chains 139 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 344 HIS B 213 HIS B 294 ASN B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5340 Z= 0.178 Angle : 0.658 9.051 7228 Z= 0.331 Chirality : 0.041 0.189 831 Planarity : 0.005 0.055 939 Dihedral : 5.355 21.537 730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.54 % Allowed : 3.96 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.32), residues: 655 helix: 0.05 (0.29), residues: 343 sheet: -3.30 (0.93), residues: 21 loop : -3.39 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 66 HIS 0.007 0.001 HIS A 90 PHE 0.017 0.002 PHE A 162 TYR 0.022 0.002 TYR A 151 ARG 0.007 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8092 (p) cc_final: 0.7671 (p) REVERT: A 97 ASP cc_start: 0.9467 (t70) cc_final: 0.9123 (t0) REVERT: A 118 LEU cc_start: 0.9091 (mm) cc_final: 0.8756 (mm) REVERT: A 151 TYR cc_start: 0.7257 (p90) cc_final: 0.5862 (p90) REVERT: A 221 MET cc_start: 0.8839 (tpt) cc_final: 0.8413 (tpt) REVERT: A 233 ASP cc_start: 0.7990 (p0) cc_final: 0.7728 (p0) REVERT: A 247 TYR cc_start: 0.8599 (m-80) cc_final: 0.8270 (m-80) REVERT: A 317 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 328 GLU cc_start: 0.8234 (pt0) cc_final: 0.7988 (pt0) REVERT: B 205 ARG cc_start: 0.7601 (mmm160) cc_final: 0.6529 (mmt180) REVERT: B 241 ASN cc_start: 0.8529 (p0) cc_final: 0.6985 (p0) REVERT: B 243 MET cc_start: 0.8061 (ppp) cc_final: 0.7822 (tmm) outliers start: 3 outliers final: 0 residues processed: 174 average time/residue: 0.1986 time to fit residues: 45.9437 Evaluate side-chains 136 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 344 HIS B 244 HIS B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5340 Z= 0.244 Angle : 0.687 8.007 7228 Z= 0.350 Chirality : 0.042 0.158 831 Planarity : 0.005 0.050 939 Dihedral : 5.449 24.365 730 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % 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: -2.08 (0.32), residues: 655 helix: 0.19 (0.29), residues: 343 sheet: -3.26 (0.89), residues: 21 loop : -3.32 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 66 HIS 0.005 0.001 HIS A 90 PHE 0.020 0.002 PHE A 163 TYR 0.019 0.002 TYR A 151 ARG 0.006 0.001 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8601 (ptp90) cc_final: 0.8344 (ptp90) REVERT: A 94 CYS cc_start: 0.8276 (p) cc_final: 0.7877 (p) REVERT: A 97 ASP cc_start: 0.9486 (t70) cc_final: 0.9115 (t0) REVERT: A 118 LEU cc_start: 0.9150 (mm) cc_final: 0.8860 (mm) REVERT: A 125 VAL cc_start: 0.9298 (m) cc_final: 0.9059 (p) REVERT: A 151 TYR cc_start: 0.7753 (p90) cc_final: 0.6283 (p90) REVERT: A 194 ASP cc_start: 0.9070 (m-30) cc_final: 0.8859 (m-30) REVERT: A 229 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8258 (t0) REVERT: A 233 ASP cc_start: 0.8098 (p0) cc_final: 0.7869 (p0) REVERT: A 317 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 328 GLU cc_start: 0.8165 (pt0) cc_final: 0.7942 (pt0) REVERT: A 356 LEU cc_start: 0.9250 (mp) cc_final: 0.8773 (mp) REVERT: B 205 ARG cc_start: 0.7708 (mmm160) cc_final: 0.6549 (mmt180) REVERT: B 277 LYS cc_start: 0.8986 (mppt) cc_final: 0.8769 (mmtt) REVERT: B 311 ASN cc_start: 0.7444 (t0) cc_final: 0.7060 (m-40) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1718 time to fit residues: 36.9590 Evaluate side-chains 135 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5340 Z= 0.181 Angle : 0.683 9.390 7228 Z= 0.339 Chirality : 0.042 0.225 831 Planarity : 0.005 0.049 939 Dihedral : 5.212 24.080 730 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: -1.92 (0.33), residues: 655 helix: 0.32 (0.29), residues: 343 sheet: -3.10 (0.95), residues: 21 loop : -3.23 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.009 0.001 HIS B 244 PHE 0.016 0.002 PHE B 250 TYR 0.038 0.002 TYR A 434 ARG 0.006 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8663 (ptp90) cc_final: 0.8446 (ptt-90) REVERT: A 94 CYS cc_start: 0.8295 (p) cc_final: 0.7847 (p) REVERT: A 97 ASP cc_start: 0.9419 (t70) cc_final: 0.9033 (t0) REVERT: A 111 MET cc_start: 0.7885 (mmt) cc_final: 0.7555 (mmt) REVERT: A 118 LEU cc_start: 0.9101 (mm) cc_final: 0.8795 (mm) REVERT: A 125 VAL cc_start: 0.9252 (m) cc_final: 0.9049 (p) REVERT: A 151 TYR cc_start: 0.7671 (p90) cc_final: 0.6054 (p90) REVERT: A 194 ASP cc_start: 0.9028 (m-30) cc_final: 0.8823 (m-30) REVERT: A 233 ASP cc_start: 0.8027 (p0) cc_final: 0.7756 (p0) REVERT: A 317 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 328 GLU cc_start: 0.8011 (pt0) cc_final: 0.7607 (pt0) REVERT: A 434 TYR cc_start: 0.6448 (m-10) cc_final: 0.5888 (m-10) REVERT: B 205 ARG cc_start: 0.7559 (mmm160) cc_final: 0.6437 (mmt180) REVERT: B 241 ASN cc_start: 0.8094 (p0) cc_final: 0.7735 (p0) REVERT: B 243 MET cc_start: 0.7725 (tmm) cc_final: 0.7399 (tmm) REVERT: B 306 GLN cc_start: 0.9078 (mm110) cc_final: 0.8588 (mp10) REVERT: B 311 ASN cc_start: 0.7390 (t0) cc_final: 0.7005 (m-40) REVERT: B 340 THR cc_start: 0.9467 (m) cc_final: 0.9068 (t) REVERT: B 346 ASN cc_start: 0.8589 (t0) cc_final: 0.8061 (t0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1581 time to fit residues: 35.3785 Evaluate side-chains 133 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 344 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5340 Z= 0.181 Angle : 0.671 8.104 7228 Z= 0.335 Chirality : 0.042 0.219 831 Planarity : 0.005 0.050 939 Dihedral : 5.104 23.207 730 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.32), residues: 655 helix: 0.34 (0.29), residues: 347 sheet: -3.20 (0.92), residues: 21 loop : -3.25 (0.32), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.008 0.001 HIS A 344 PHE 0.015 0.001 PHE A 163 TYR 0.028 0.002 TYR A 434 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8647 (ptp90) cc_final: 0.8432 (ptt-90) REVERT: A 94 CYS cc_start: 0.8287 (p) cc_final: 0.7823 (p) REVERT: A 97 ASP cc_start: 0.9415 (t70) cc_final: 0.9042 (t0) REVERT: A 111 MET cc_start: 0.7871 (mmt) cc_final: 0.7574 (mmt) REVERT: A 125 VAL cc_start: 0.9291 (m) cc_final: 0.9085 (p) REVERT: A 151 TYR cc_start: 0.7676 (p90) cc_final: 0.6084 (p90) REVERT: A 233 ASP cc_start: 0.7999 (p0) cc_final: 0.7752 (p0) REVERT: A 317 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 356 LEU cc_start: 0.8789 (mp) cc_final: 0.8332 (tt) REVERT: A 434 TYR cc_start: 0.6578 (m-10) cc_final: 0.6230 (m-10) REVERT: B 205 ARG cc_start: 0.7568 (mmm160) cc_final: 0.6474 (mmt180) REVERT: B 241 ASN cc_start: 0.8023 (p0) cc_final: 0.7411 (p0) REVERT: B 243 MET cc_start: 0.7798 (tmm) cc_final: 0.7441 (tmm) REVERT: B 244 HIS cc_start: 0.8377 (m-70) cc_final: 0.8147 (m90) REVERT: B 247 MET cc_start: 0.8629 (mtt) cc_final: 0.8227 (mtt) REVERT: B 277 LYS cc_start: 0.8952 (mppt) cc_final: 0.8733 (mmtt) REVERT: B 306 GLN cc_start: 0.9118 (mm110) cc_final: 0.8651 (mp10) REVERT: B 311 ASN cc_start: 0.7373 (t0) cc_final: 0.6939 (m-40) REVERT: B 340 THR cc_start: 0.9438 (m) cc_final: 0.9034 (t) REVERT: B 347 ASN cc_start: 0.8933 (m-40) cc_final: 0.8621 (m-40) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1752 time to fit residues: 39.2634 Evaluate side-chains 132 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN A 229 ASN A 344 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5340 Z= 0.179 Angle : 0.702 10.614 7228 Z= 0.343 Chirality : 0.042 0.227 831 Planarity : 0.005 0.053 939 Dihedral : 5.092 23.810 730 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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 (0.33), residues: 655 helix: 0.50 (0.29), residues: 344 sheet: -2.96 (0.96), residues: 21 loop : -3.15 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.008 0.001 HIS A 344 PHE 0.018 0.001 PHE A 163 TYR 0.028 0.002 TYR A 434 ARG 0.004 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8648 (ptp90) cc_final: 0.8422 (ptt-90) REVERT: A 94 CYS cc_start: 0.8357 (p) cc_final: 0.7908 (p) REVERT: A 97 ASP cc_start: 0.9400 (t70) cc_final: 0.9056 (t0) REVERT: A 118 LEU cc_start: 0.9142 (mm) cc_final: 0.8783 (mm) REVERT: A 151 TYR cc_start: 0.7770 (p90) cc_final: 0.6346 (p90) REVERT: A 224 LEU cc_start: 0.9547 (mt) cc_final: 0.9266 (mt) REVERT: A 233 ASP cc_start: 0.8043 (p0) cc_final: 0.7729 (p0) REVERT: A 247 TYR cc_start: 0.8675 (m-80) cc_final: 0.8304 (m-80) REVERT: A 317 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 328 GLU cc_start: 0.7937 (pt0) cc_final: 0.7659 (pt0) REVERT: A 356 LEU cc_start: 0.8826 (mp) cc_final: 0.8294 (tt) REVERT: A 425 MET cc_start: 0.8047 (pmm) cc_final: 0.7738 (pmm) REVERT: A 434 TYR cc_start: 0.6123 (m-10) cc_final: 0.5876 (m-10) REVERT: B 241 ASN cc_start: 0.7980 (p0) cc_final: 0.7720 (p0) REVERT: B 247 MET cc_start: 0.8609 (mtt) cc_final: 0.8303 (mtt) REVERT: B 265 ILE cc_start: 0.8195 (mm) cc_final: 0.7940 (mm) REVERT: B 306 GLN cc_start: 0.9109 (mm110) cc_final: 0.8647 (mp10) REVERT: B 311 ASN cc_start: 0.7266 (t0) cc_final: 0.6855 (m-40) REVERT: B 340 THR cc_start: 0.9454 (m) cc_final: 0.9060 (t) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1518 time to fit residues: 33.8247 Evaluate side-chains 134 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 229 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5340 Z= 0.203 Angle : 0.717 9.450 7228 Z= 0.356 Chirality : 0.044 0.175 831 Planarity : 0.005 0.051 939 Dihedral : 5.188 29.097 730 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.18 % Allowed : 0.72 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.33), residues: 655 helix: 0.56 (0.29), residues: 344 sheet: -2.74 (0.99), residues: 21 loop : -3.20 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 66 HIS 0.009 0.001 HIS A 344 PHE 0.017 0.001 PHE A 163 TYR 0.030 0.002 TYR A 434 ARG 0.005 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8727 (mmm-85) REVERT: A 94 CYS cc_start: 0.8371 (p) cc_final: 0.7900 (p) REVERT: A 97 ASP cc_start: 0.9404 (t70) cc_final: 0.9041 (t0) REVERT: A 171 LEU cc_start: 0.8961 (mt) cc_final: 0.8748 (mt) REVERT: A 233 ASP cc_start: 0.8042 (p0) cc_final: 0.7763 (p0) REVERT: A 247 TYR cc_start: 0.8722 (m-80) cc_final: 0.8438 (m-80) REVERT: A 317 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 328 GLU cc_start: 0.7966 (pt0) cc_final: 0.7728 (pt0) REVERT: A 356 LEU cc_start: 0.9007 (mp) cc_final: 0.8453 (tt) REVERT: A 380 MET cc_start: 0.8750 (ptp) cc_final: 0.8185 (ptm) REVERT: A 425 MET cc_start: 0.7938 (pmm) cc_final: 0.7615 (pmm) REVERT: A 434 TYR cc_start: 0.6190 (m-10) cc_final: 0.5893 (m-10) REVERT: B 241 ASN cc_start: 0.7970 (p0) cc_final: 0.7649 (p0) REVERT: B 243 MET cc_start: 0.7918 (tmm) cc_final: 0.7572 (tmm) REVERT: B 244 HIS cc_start: 0.8470 (m-70) cc_final: 0.8099 (m90) REVERT: B 247 MET cc_start: 0.8560 (mtt) cc_final: 0.8209 (mtt) REVERT: B 311 ASN cc_start: 0.7234 (t0) cc_final: 0.6854 (m-40) REVERT: B 340 THR cc_start: 0.9448 (m) cc_final: 0.9021 (t) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.1999 time to fit residues: 43.3328 Evaluate side-chains 134 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 41 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5340 Z= 0.178 Angle : 0.711 9.168 7228 Z= 0.347 Chirality : 0.042 0.196 831 Planarity : 0.005 0.050 939 Dihedral : 5.070 26.294 730 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -1.56 (0.33), residues: 655 helix: 0.69 (0.29), residues: 338 sheet: -2.59 (1.02), residues: 21 loop : -3.14 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.006 0.001 HIS A 273 PHE 0.014 0.001 PHE A 163 TYR 0.024 0.002 TYR A 434 ARG 0.005 0.000 ARG A 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9411 (mt) cc_final: 0.9188 (mt) REVERT: A 94 CYS cc_start: 0.8424 (p) cc_final: 0.7970 (p) REVERT: A 97 ASP cc_start: 0.9384 (t70) cc_final: 0.9027 (t0) REVERT: A 116 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 118 LEU cc_start: 0.9089 (mm) cc_final: 0.8730 (mm) REVERT: A 224 LEU cc_start: 0.9561 (mt) cc_final: 0.9299 (mt) REVERT: A 233 ASP cc_start: 0.8062 (p0) cc_final: 0.7682 (p0) REVERT: A 247 TYR cc_start: 0.8684 (m-80) cc_final: 0.8351 (m-80) REVERT: A 317 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 425 MET cc_start: 0.7892 (pmm) cc_final: 0.7587 (pmm) REVERT: A 434 TYR cc_start: 0.6132 (m-10) cc_final: 0.5885 (m-10) REVERT: B 34 VAL cc_start: 0.8339 (m) cc_final: 0.7914 (p) REVERT: B 205 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7474 (mmt180) REVERT: B 241 ASN cc_start: 0.7778 (p0) cc_final: 0.7203 (p0) REVERT: B 243 MET cc_start: 0.7918 (tmm) cc_final: 0.7595 (tmm) REVERT: B 244 HIS cc_start: 0.8439 (m-70) cc_final: 0.8179 (m90) REVERT: B 247 MET cc_start: 0.8521 (mtt) cc_final: 0.8179 (mtt) REVERT: B 275 GLU cc_start: 0.8449 (mp0) cc_final: 0.8178 (mp0) REVERT: B 277 LYS cc_start: 0.8847 (mppt) cc_final: 0.8622 (mmtm) REVERT: B 311 ASN cc_start: 0.7168 (t0) cc_final: 0.6795 (m-40) REVERT: B 340 THR cc_start: 0.9442 (m) cc_final: 0.9045 (t) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1839 time to fit residues: 40.7907 Evaluate side-chains 134 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 0.0670 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 229 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097184 restraints weight = 12582.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099932 restraints weight = 8522.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101912 restraints weight = 6485.334| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5340 Z= 0.279 Angle : 0.796 9.490 7228 Z= 0.397 Chirality : 0.046 0.144 831 Planarity : 0.005 0.057 939 Dihedral : 5.476 29.080 730 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.18 % Allowed : 0.72 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.32), residues: 655 helix: 0.52 (0.29), residues: 339 sheet: -2.80 (0.94), residues: 21 loop : -3.27 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 258 HIS 0.014 0.002 HIS A 344 PHE 0.015 0.002 PHE A 163 TYR 0.038 0.003 TYR A 151 ARG 0.007 0.001 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.97 seconds wall clock time: 31 minutes 12.45 seconds (1872.45 seconds total)