Starting phenix.real_space_refine on Sun Mar 10 21:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/03_2024/6vu8_21388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/03_2024/6vu8_21388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/03_2024/6vu8_21388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/03_2024/6vu8_21388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu8_21388/03_2024/6vu8_21388_updated.pdb" } 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 Residue "A ASP 8": "OD1" <-> "OD2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.60, per 1000 atoms: 0.69 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 - 3.50 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... running ksdssp... Secondary structure from input PDB file: 29 helices and 1 sheets defined 48.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 15 through 28 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 40 through 56 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 86 through 96 Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 241 through 259 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) Processing helix chain 'A' and resid 267 through 279 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) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 345 through 355 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 372 through 381 removed outlier: 3.886A pdb=" N ARG A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 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 412 through 422 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 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 335 through 350 removed outlier: 4.238A pdb=" N ALA B 338 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 339 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 350 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.036A pdb=" N GLU B 318 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 266 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR B 320 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 268 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS B 322 " --> pdb=" O LEU B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 192 hydrogen bonds defined for protein. 546 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: 1.48 Time building geometry restraints manager: 2.33 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: 97.80 - 105.05: 83 105.05 - 112.30: 2604 112.30 - 119.55: 1960 119.55 - 126.80: 2523 126.80 - 134.05: 58 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: 1331 2.79 - 3.32: 5068 3.32 - 3.84: 8478 3.84 - 4.37: 9470 4.37 - 4.90: 15265 Nonbonded interactions: 39612 Sorted by model distance: nonbonded pdb=" O PHE A 270 " pdb=" OG1 THR A 274 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU A 197 " pdb=" OH TYR A 249 " model vdw 2.313 2.440 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 260 " model vdw 2.317 2.440 nonbonded pdb=" O PHE A 406 " pdb=" OG1 THR A 410 " model vdw 2.326 2.440 nonbonded pdb=" NH2 ARG A 255 " pdb=" O LEU A 286 " model vdw 2.334 2.520 ... (remaining 39607 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=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: 0.240 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: 1.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.360 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- 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= 0.381 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 fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.621 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: 0.1674 time to fit residues: 37.8224 Evaluate side-chains 136 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 90 HIS A 229 ASN A 344 HIS B 304 GLN B 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1966 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= 0.179 Angle : 0.634 7.530 7228 Z= 0.329 Chirality : 0.039 0.155 831 Planarity : 0.005 0.054 939 Dihedral : 6.094 25.217 730 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.36 % Allowed : 5.77 % Favored : 93.87 % 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: -3.11 (0.30), residues: 655 helix: -0.95 (0.27), residues: 334 sheet: -3.51 (0.94), residues: 21 loop : -3.33 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 258 HIS 0.006 0.001 HIS A 344 PHE 0.012 0.002 PHE A 394 TYR 0.014 0.002 TYR A 151 ARG 0.007 0.000 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 176 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7546 (mp0) cc_final: 0.7302 (pm20) REVERT: A 16 ASP cc_start: 0.8666 (p0) cc_final: 0.8464 (p0) REVERT: A 27 ARG cc_start: 0.8950 (ptm160) cc_final: 0.8633 (ptp90) REVERT: A 66 TRP cc_start: 0.8622 (m-90) cc_final: 0.8410 (m-90) REVERT: A 90 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8259 (t-90) REVERT: A 97 ASP cc_start: 0.9505 (t70) cc_final: 0.9143 (t0) REVERT: A 163 PHE cc_start: 0.9213 (m-80) cc_final: 0.8995 (m-80) REVERT: A 194 ASP cc_start: 0.8993 (m-30) cc_final: 0.8644 (m-30) REVERT: A 233 ASP cc_start: 0.7916 (p0) cc_final: 0.7664 (p0) REVERT: A 247 TYR cc_start: 0.8450 (m-80) cc_final: 0.8184 (m-10) REVERT: A 270 PHE cc_start: 0.9174 (t80) cc_final: 0.8948 (t80) REVERT: A 328 GLU cc_start: 0.8284 (pt0) cc_final: 0.7983 (pt0) REVERT: A 396 PHE cc_start: 0.8335 (t80) cc_final: 0.7952 (t80) REVERT: A 445 TYR cc_start: 0.8073 (t80) cc_final: 0.7867 (t80) REVERT: B 205 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6417 (mmt180) REVERT: B 241 ASN cc_start: 0.8836 (p0) cc_final: 0.7274 (p0) REVERT: B 243 MET cc_start: 0.7970 (ppp) cc_final: 0.7446 (tmm) REVERT: B 244 HIS cc_start: 0.8813 (m-70) cc_final: 0.8190 (m-70) REVERT: B 247 MET cc_start: 0.8493 (mtt) cc_final: 0.8143 (mtt) REVERT: B 296 TYR cc_start: 0.8382 (t80) cc_final: 0.8175 (t80) REVERT: B 340 THR cc_start: 0.9358 (m) cc_final: 0.9100 (t) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.1443 time to fit residues: 33.6340 Evaluate side-chains 147 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 48 optimal weight: 7.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS B 244 HIS B 256 ASN B 304 GLN B 322 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2488 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= 0.175 Angle : 0.638 8.229 7228 Z= 0.324 Chirality : 0.040 0.158 831 Planarity : 0.005 0.067 939 Dihedral : 5.673 23.436 730 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.36 % Allowed : 6.31 % Favored : 93.33 % 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: -2.53 (0.32), residues: 655 helix: -0.36 (0.28), residues: 336 sheet: -3.36 (0.95), residues: 21 loop : -3.22 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 258 HIS 0.009 0.001 HIS A 90 PHE 0.013 0.001 PHE A 163 TYR 0.030 0.002 TYR A 434 ARG 0.005 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 176 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TRP cc_start: 0.8627 (m-90) cc_final: 0.8427 (m-90) REVERT: A 94 CYS cc_start: 0.7995 (p) cc_final: 0.7655 (p) REVERT: A 97 ASP cc_start: 0.9497 (t70) cc_final: 0.9150 (t0) REVERT: A 111 MET cc_start: 0.8226 (mmt) cc_final: 0.7972 (mpp) REVERT: A 118 LEU cc_start: 0.9111 (mm) cc_final: 0.8899 (mm) REVERT: A 133 MET cc_start: 0.8726 (tmm) cc_final: 0.8525 (tmm) REVERT: A 170 LEU cc_start: 0.9214 (mt) cc_final: 0.9001 (mt) REVERT: A 191 LEU cc_start: 0.9008 (pp) cc_final: 0.8619 (pp) REVERT: A 194 ASP cc_start: 0.9159 (m-30) cc_final: 0.8889 (m-30) REVERT: A 233 ASP cc_start: 0.7984 (p0) cc_final: 0.7687 (p0) REVERT: A 247 TYR cc_start: 0.8537 (m-80) cc_final: 0.8257 (m-80) REVERT: A 328 GLU cc_start: 0.8352 (pt0) cc_final: 0.7907 (pt0) REVERT: B 205 ARG cc_start: 0.7433 (mmm160) cc_final: 0.6383 (mmt180) REVERT: B 241 ASN cc_start: 0.8565 (p0) cc_final: 0.7305 (p0) REVERT: B 243 MET cc_start: 0.8060 (ppp) cc_final: 0.7692 (tmm) REVERT: B 244 HIS cc_start: 0.8488 (m90) cc_final: 0.7819 (m-70) REVERT: B 247 MET cc_start: 0.8684 (mtt) cc_final: 0.8162 (mtt) REVERT: B 340 THR cc_start: 0.9363 (m) cc_final: 0.9152 (t) REVERT: B 346 ASN cc_start: 0.8142 (t0) cc_final: 0.7723 (t0) REVERT: B 350 ASP cc_start: 0.7215 (m-30) cc_final: 0.6966 (m-30) REVERT: B 354 PHE cc_start: 0.7130 (p90) cc_final: 0.6541 (p90) outliers start: 2 outliers final: 0 residues processed: 174 average time/residue: 0.1538 time to fit residues: 35.0216 Evaluate side-chains 146 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 0.0870 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.0470 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 304 GLN B 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5340 Z= 0.149 Angle : 0.627 7.985 7228 Z= 0.313 Chirality : 0.039 0.135 831 Planarity : 0.005 0.055 939 Dihedral : 5.320 23.378 730 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % 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: -2.16 (0.33), residues: 655 helix: -0.03 (0.29), residues: 341 sheet: -2.86 (1.17), residues: 16 loop : -3.15 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 258 HIS 0.006 0.001 HIS A 90 PHE 0.017 0.001 PHE A 162 TYR 0.018 0.002 TYR A 434 ARG 0.004 0.000 ARG A 458 *********************** 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 187 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8214 (p) cc_final: 0.7842 (p) REVERT: A 97 ASP cc_start: 0.9498 (t70) cc_final: 0.9292 (t0) REVERT: A 118 LEU cc_start: 0.9136 (mm) cc_final: 0.8862 (mm) REVERT: A 125 VAL cc_start: 0.9281 (m) cc_final: 0.9042 (p) REVERT: A 133 MET cc_start: 0.8698 (tmm) cc_final: 0.8495 (tmm) REVERT: A 194 ASP cc_start: 0.9111 (m-30) cc_final: 0.8890 (m-30) REVERT: A 197 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8370 (mt-10) REVERT: A 233 ASP cc_start: 0.7912 (p0) cc_final: 0.7598 (p0) REVERT: A 317 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 328 GLU cc_start: 0.8287 (pt0) cc_final: 0.7750 (pt0) REVERT: A 356 LEU cc_start: 0.8836 (mp) cc_final: 0.8207 (mp) REVERT: A 383 LEU cc_start: 0.8441 (pt) cc_final: 0.8201 (pp) REVERT: A 409 TYR cc_start: 0.6871 (t80) cc_final: 0.6658 (t80) REVERT: B 34 VAL cc_start: 0.8585 (m) cc_final: 0.8311 (m) REVERT: B 205 ARG cc_start: 0.7530 (mmm160) cc_final: 0.6514 (mmt180) REVERT: B 241 ASN cc_start: 0.8247 (p0) cc_final: 0.7603 (p0) REVERT: B 247 MET cc_start: 0.8783 (mtt) cc_final: 0.8342 (mtt) REVERT: B 340 THR cc_start: 0.9320 (m) cc_final: 0.9118 (t) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1567 time to fit residues: 38.0995 Evaluate side-chains 144 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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: 10.0000 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS A 344 HIS B 322 HIS ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5340 Z= 0.276 Angle : 0.715 9.574 7228 Z= 0.363 Chirality : 0.042 0.134 831 Planarity : 0.005 0.048 939 Dihedral : 5.534 22.317 730 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.36 % Allowed : 3.24 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.33), residues: 655 helix: 0.02 (0.30), residues: 333 sheet: -3.38 (0.95), residues: 21 loop : -3.11 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.006 0.001 HIS A 90 PHE 0.024 0.002 PHE A 163 TYR 0.016 0.002 TYR A 247 ARG 0.005 0.000 ARG A 458 *********************** 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 173 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8278 (p) cc_final: 0.7904 (p) REVERT: A 97 ASP cc_start: 0.9513 (t70) cc_final: 0.9140 (t0) REVERT: A 118 LEU cc_start: 0.9143 (mm) cc_final: 0.8832 (mm) REVERT: A 194 ASP cc_start: 0.9113 (m-30) cc_final: 0.8814 (m-30) REVERT: A 197 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8507 (pt0) REVERT: A 224 LEU cc_start: 0.9455 (mt) cc_final: 0.8997 (mt) REVERT: A 229 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8247 (t0) REVERT: A 233 ASP cc_start: 0.7986 (p0) cc_final: 0.7664 (p0) REVERT: A 317 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7628 (mm-30) REVERT: A 328 GLU cc_start: 0.8226 (pt0) cc_final: 0.7939 (pt0) REVERT: B 205 ARG cc_start: 0.7456 (mmm160) cc_final: 0.6430 (mmt180) REVERT: B 229 ASP cc_start: 0.8681 (p0) cc_final: 0.8448 (p0) REVERT: B 241 ASN cc_start: 0.8546 (p0) cc_final: 0.8134 (p0) REVERT: B 243 MET cc_start: 0.8276 (tmm) cc_final: 0.8074 (tmm) REVERT: B 244 HIS cc_start: 0.8484 (m170) cc_final: 0.8002 (m170) REVERT: B 247 MET cc_start: 0.8789 (mtt) cc_final: 0.8323 (mtt) REVERT: B 265 ILE cc_start: 0.8412 (mm) cc_final: 0.8196 (mm) REVERT: B 277 LYS cc_start: 0.8992 (mppt) cc_final: 0.8754 (mmtt) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.1416 time to fit residues: 32.3421 Evaluate side-chains 142 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 0.0970 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 414 ASN B 304 GLN B 322 HIS ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3476 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= 0.210 Angle : 0.679 8.133 7228 Z= 0.344 Chirality : 0.041 0.137 831 Planarity : 0.005 0.052 939 Dihedral : 5.436 27.896 730 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.18 % Allowed : 4.32 % 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: -2.03 (0.33), residues: 655 helix: 0.09 (0.29), residues: 339 sheet: -3.42 (0.95), residues: 21 loop : -3.01 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.004 0.001 HIS A 90 PHE 0.015 0.002 PHE B 196 TYR 0.034 0.002 TYR A 434 ARG 0.008 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 175 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8344 (p) cc_final: 0.7909 (p) REVERT: A 97 ASP cc_start: 0.9507 (t70) cc_final: 0.9137 (t0) REVERT: A 111 MET cc_start: 0.8213 (mmt) cc_final: 0.7943 (mmt) REVERT: A 194 ASP cc_start: 0.9095 (m-30) cc_final: 0.8795 (m-30) REVERT: A 197 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8495 (pt0) REVERT: A 233 ASP cc_start: 0.7916 (p0) cc_final: 0.7607 (p0) REVERT: A 254 LEU cc_start: 0.9478 (tt) cc_final: 0.8983 (tp) REVERT: A 270 PHE cc_start: 0.9207 (t80) cc_final: 0.8919 (t80) REVERT: A 328 GLU cc_start: 0.8246 (pt0) cc_final: 0.7944 (pt0) REVERT: A 425 MET cc_start: 0.7975 (pmm) cc_final: 0.7712 (pmm) REVERT: B 205 ARG cc_start: 0.7467 (mmm160) cc_final: 0.6415 (mmt180) REVERT: B 241 ASN cc_start: 0.8303 (p0) cc_final: 0.8084 (p0) REVERT: B 243 MET cc_start: 0.8178 (tmm) cc_final: 0.7930 (tmm) REVERT: B 244 HIS cc_start: 0.8390 (m170) cc_final: 0.7918 (m170) REVERT: B 247 MET cc_start: 0.8777 (mtt) cc_final: 0.8270 (mtt) REVERT: B 277 LYS cc_start: 0.9055 (mppt) cc_final: 0.8844 (mmtt) REVERT: B 340 THR cc_start: 0.9390 (m) cc_final: 0.9173 (t) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1451 time to fit residues: 33.9164 Evaluate side-chains 141 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 322 HIS B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3773 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= 0.176 Angle : 0.669 9.983 7228 Z= 0.333 Chirality : 0.041 0.164 831 Planarity : 0.005 0.055 939 Dihedral : 5.252 27.403 730 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.54 % Allowed : 2.34 % 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: -1.77 (0.34), residues: 655 helix: 0.31 (0.30), residues: 342 sheet: -3.22 (0.97), residues: 21 loop : -2.94 (0.35), residues: 292 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 0.002 PHE A 163 TYR 0.015 0.002 TYR A 434 ARG 0.005 0.000 ARG A 348 *********************** 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 179 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8357 (p) cc_final: 0.7915 (p) REVERT: A 97 ASP cc_start: 0.9506 (t70) cc_final: 0.9123 (t0) REVERT: A 111 MET cc_start: 0.8112 (mmt) cc_final: 0.7884 (mmt) REVERT: A 194 ASP cc_start: 0.9014 (m-30) cc_final: 0.8770 (m-30) REVERT: A 197 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8530 (pt0) REVERT: A 233 ASP cc_start: 0.7920 (p0) cc_final: 0.7622 (p0) REVERT: A 254 LEU cc_start: 0.9372 (tt) cc_final: 0.8957 (tp) REVERT: A 270 PHE cc_start: 0.9176 (t80) cc_final: 0.8807 (t80) REVERT: A 317 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 328 GLU cc_start: 0.8235 (pt0) cc_final: 0.7875 (pt0) REVERT: A 425 MET cc_start: 0.8001 (pmm) cc_final: 0.7789 (pmm) REVERT: B 205 ARG cc_start: 0.7496 (mmm160) cc_final: 0.6514 (mmt180) REVERT: B 243 MET cc_start: 0.8214 (tmm) cc_final: 0.7866 (tmm) REVERT: B 244 HIS cc_start: 0.8416 (m170) cc_final: 0.7990 (m170) REVERT: B 247 MET cc_start: 0.8857 (mtt) cc_final: 0.8310 (mtt) REVERT: B 253 ILE cc_start: 0.8233 (mm) cc_final: 0.8006 (mm) outliers start: 3 outliers final: 0 residues processed: 176 average time/residue: 0.1438 time to fit residues: 33.6676 Evaluate side-chains 137 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 0.0970 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 229 ASN A 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5340 Z= 0.158 Angle : 0.670 8.571 7228 Z= 0.332 Chirality : 0.041 0.141 831 Planarity : 0.005 0.053 939 Dihedral : 5.097 24.052 730 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.18 % Allowed : 0.36 % Favored : 99.46 % 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: -1.64 (0.34), residues: 655 helix: 0.34 (0.29), residues: 344 sheet: -2.84 (1.02), residues: 21 loop : -2.82 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.009 0.001 HIS A 344 PHE 0.020 0.001 PHE A 163 TYR 0.036 0.002 TYR A 151 ARG 0.004 0.000 ARG A 219 *********************** 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 181 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8390 (p) cc_final: 0.7953 (p) REVERT: A 97 ASP cc_start: 0.9519 (t70) cc_final: 0.9093 (t0) REVERT: A 111 MET cc_start: 0.7887 (mmt) cc_final: 0.7655 (mmt) REVERT: A 229 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8148 (t0) REVERT: A 232 PHE cc_start: 0.8461 (p90) cc_final: 0.8234 (p90) REVERT: A 233 ASP cc_start: 0.7990 (p0) cc_final: 0.7760 (p0) REVERT: A 254 LEU cc_start: 0.9398 (tt) cc_final: 0.8955 (tp) REVERT: A 270 PHE cc_start: 0.9175 (t80) cc_final: 0.8801 (t80) REVERT: A 317 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 328 GLU cc_start: 0.8181 (pt0) cc_final: 0.7846 (pt0) REVERT: B 205 ARG cc_start: 0.7506 (mmm160) cc_final: 0.6490 (mmt180) REVERT: B 241 ASN cc_start: 0.8843 (p0) cc_final: 0.7469 (p0) REVERT: B 247 MET cc_start: 0.8622 (mtt) cc_final: 0.8174 (mtt) REVERT: B 296 TYR cc_start: 0.8542 (t80) cc_final: 0.8208 (t80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1655 time to fit residues: 39.0409 Evaluate side-chains 137 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4383 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= 0.176 Angle : 0.699 8.632 7228 Z= 0.344 Chirality : 0.041 0.142 831 Planarity : 0.005 0.055 939 Dihedral : 5.210 26.412 730 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.66 (0.34), residues: 655 helix: 0.37 (0.30), residues: 342 sheet: -2.46 (1.04), residues: 21 loop : -2.93 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.004 0.001 HIS A 158 PHE 0.018 0.001 PHE A 163 TYR 0.013 0.002 TYR A 434 ARG 0.006 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 170 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 CYS cc_start: 0.8408 (p) cc_final: 0.7959 (p) REVERT: A 97 ASP cc_start: 0.9518 (t70) cc_final: 0.9072 (t0) REVERT: A 111 MET cc_start: 0.7896 (mmt) cc_final: 0.7511 (mmt) REVERT: A 233 ASP cc_start: 0.8031 (p0) cc_final: 0.7793 (p0) REVERT: A 254 LEU cc_start: 0.9431 (tt) cc_final: 0.9108 (tp) REVERT: A 270 PHE cc_start: 0.9171 (t80) cc_final: 0.8806 (t80) REVERT: A 306 MET cc_start: 0.7821 (ttm) cc_final: 0.7571 (ttm) REVERT: A 317 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 328 GLU cc_start: 0.8189 (pt0) cc_final: 0.7808 (pt0) REVERT: A 356 LEU cc_start: 0.8912 (mp) cc_final: 0.8282 (tt) REVERT: A 380 MET cc_start: 0.8492 (ptm) cc_final: 0.8005 (ptm) REVERT: B 205 ARG cc_start: 0.7518 (mmm160) cc_final: 0.6548 (mmt180) REVERT: B 247 MET cc_start: 0.8754 (mtt) cc_final: 0.8271 (mtt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1395 time to fit residues: 31.7020 Evaluate side-chains 137 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 322 HIS ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4171 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= 0.260 Angle : 0.748 12.087 7228 Z= 0.371 Chirality : 0.043 0.164 831 Planarity : 0.005 0.053 939 Dihedral : 5.459 26.536 730 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.36 % Allowed : 0.00 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.81 (0.33), residues: 655 helix: 0.29 (0.30), residues: 332 sheet: -2.65 (1.03), residues: 21 loop : -2.92 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 66 HIS 0.018 0.002 HIS A 344 PHE 0.018 0.002 PHE A 163 TYR 0.035 0.003 TYR A 151 ARG 0.006 0.001 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 159 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8903 (ptp90) cc_final: 0.8698 (ptp90) REVERT: A 94 CYS cc_start: 0.8406 (p) cc_final: 0.7961 (p) REVERT: A 111 MET cc_start: 0.7906 (mmt) cc_final: 0.7551 (mmt) REVERT: A 123 ASN cc_start: 0.7930 (m-40) cc_final: 0.7540 (m110) REVERT: A 270 PHE cc_start: 0.9219 (t80) cc_final: 0.8959 (t80) REVERT: A 317 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 328 GLU cc_start: 0.8160 (pt0) cc_final: 0.7722 (pt0) REVERT: A 425 MET cc_start: 0.7702 (pmm) cc_final: 0.7442 (pmm) REVERT: B 205 ARG cc_start: 0.7672 (mmm160) cc_final: 0.6585 (mmt180) REVERT: B 247 MET cc_start: 0.8734 (mtt) cc_final: 0.8298 (mtt) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.1342 time to fit residues: 28.3609 Evaluate side-chains 128 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 229 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099138 restraints weight = 12494.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101828 restraints weight = 8518.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103650 restraints weight = 6506.513| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5340 Z= 0.197 Angle : 0.726 11.417 7228 Z= 0.352 Chirality : 0.042 0.156 831 Planarity : 0.005 0.053 939 Dihedral : 5.309 26.573 730 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.34), residues: 655 helix: 0.36 (0.30), residues: 334 sheet: -2.47 (1.09), residues: 21 loop : -2.92 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.012 0.001 HIS A 158 PHE 0.015 0.001 PHE A 163 TYR 0.035 0.003 TYR A 151 ARG 0.008 0.000 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.45 seconds wall clock time: 28 minutes 8.60 seconds (1688.60 seconds total)