Starting phenix.real_space_refine on Fri Jul 19 09:39:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qlo_18486/07_2024/8qlo_18486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qlo_18486/07_2024/8qlo_18486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qlo_18486/07_2024/8qlo_18486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qlo_18486/07_2024/8qlo_18486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qlo_18486/07_2024/8qlo_18486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qlo_18486/07_2024/8qlo_18486.cif" } resolution = 2.57 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= 0.008 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4726 2.51 5 N 1203 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7282 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3657 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3625 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 419} Time building chain proxies: 5.31, per 1000 atoms: 0.73 Number of scatterers: 7282 At special positions: 0 Unit cell: (80.6, 81.25, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1331 8.00 N 1203 7.00 C 4726 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 41.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.580A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.731A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.694A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.688A pdb=" N ALA B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.612A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.731A pdb=" N LEU B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.258A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.706A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.743A pdb=" N ILE A 113 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.721A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 222 through 226 removed outlier: 4.330A pdb=" N HIS A 225 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'A' and resid 423 through 436 Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.430A pdb=" N LYS B 2 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.607A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE B 443 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 386 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.116A pdb=" N SER B 41 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 44 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AA7, first strand: chain 'B' and resid 425 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 31 through 33 removed outlier: 8.307A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER A 8 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AB1, first strand: chain 'A' and resid 283 through 285 removed outlier: 7.438A pdb=" N TRP A 175 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU A 406 " --> pdb=" O TRP A 175 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'A' and resid 304 through 305 338 hydrogen bonds defined for protein. 912 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: 2.27 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1216 1.30 - 1.43: 1942 1.43 - 1.55: 4274 1.55 - 1.68: 0 1.68 - 1.81: 34 Bond restraints: 7466 Sorted by residual: bond pdb=" C PRO B 404 " pdb=" O PRO B 404 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.30e-02 5.92e+03 2.55e+01 bond pdb=" C PRO B 268 " pdb=" O PRO B 268 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.25e+01 bond pdb=" C PRO B 76 " pdb=" O PRO B 76 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.35e-02 5.49e+03 2.24e+01 bond pdb=" CA TYR B 425 " pdb=" C TYR B 425 " ideal model delta sigma weight residual 1.521 1.471 0.051 1.19e-02 7.06e+03 1.81e+01 bond pdb=" C PRO B 499 " pdb=" O PRO B 499 " ideal model delta sigma weight residual 1.240 1.193 0.047 1.12e-02 7.97e+03 1.78e+01 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.18: 159 105.18 - 112.55: 3656 112.55 - 119.92: 3054 119.92 - 127.29: 3144 127.29 - 134.67: 77 Bond angle restraints: 10090 Sorted by residual: angle pdb=" N LEU A 37 " pdb=" CA LEU A 37 " pdb=" C LEU A 37 " ideal model delta sigma weight residual 113.15 104.98 8.17 1.19e+00 7.06e-01 4.72e+01 angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" C PRO B 499 " ideal model delta sigma weight residual 110.70 103.30 7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 113.07 105.02 8.05 1.36e+00 5.41e-01 3.51e+01 angle pdb=" N TYR B 472 " pdb=" CA TYR B 472 " pdb=" C TYR B 472 " ideal model delta sigma weight residual 111.33 104.31 7.02 1.21e+00 6.83e-01 3.37e+01 angle pdb=" N ILE B 70 " pdb=" CA ILE B 70 " pdb=" C ILE B 70 " ideal model delta sigma weight residual 111.56 106.68 4.88 8.60e-01 1.35e+00 3.22e+01 ... (remaining 10085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 3833 14.89 - 29.79: 441 29.79 - 44.68: 141 44.68 - 59.57: 37 59.57 - 74.47: 21 Dihedral angle restraints: 4473 sinusoidal: 1858 harmonic: 2615 Sorted by residual: dihedral pdb=" C TYR B 425 " pdb=" N TYR B 425 " pdb=" CA TYR B 425 " pdb=" CB TYR B 425 " ideal model delta harmonic sigma weight residual -122.60 -111.27 -11.33 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" CA ARG B 213 " pdb=" C ARG B 213 " pdb=" N LEU B 214 " pdb=" CA LEU B 214 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" N ALA A 63 " pdb=" C ALA A 63 " pdb=" CA ALA A 63 " pdb=" CB ALA A 63 " ideal model delta harmonic sigma weight residual 122.90 114.66 8.24 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 4470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 633 0.051 - 0.103: 238 0.103 - 0.154: 137 0.154 - 0.205: 58 0.205 - 0.257: 10 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA VAL B 423 " pdb=" N VAL B 423 " pdb=" C VAL B 423 " pdb=" CB VAL B 423 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 334 " pdb=" CA VAL A 334 " pdb=" CG1 VAL A 334 " pdb=" CG2 VAL A 334 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 122 " pdb=" N ILE B 122 " pdb=" C ILE B 122 " pdb=" CB ILE B 122 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1073 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 40 " 0.016 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LYS B 40 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS B 40 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 41 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 24 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.09e+00 pdb=" NE ARG B 24 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 24 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 24 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 315 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C GLY B 315 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY B 315 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU B 316 " -0.014 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 742 2.75 - 3.29: 7331 3.29 - 3.82: 12272 3.82 - 4.36: 15855 4.36 - 4.90: 25514 Nonbonded interactions: 61714 Sorted by model distance: nonbonded pdb=" N GLU A 284 " pdb=" OE1 GLU A 284 " model vdw 2.209 2.520 nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 230 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASN B 307 " pdb=" N ASP B 309 " model vdw 2.264 2.520 nonbonded pdb=" N GLU B 132 " pdb=" OE1 GLU B 132 " model vdw 2.296 2.520 nonbonded pdb=" OG SER A 173 " pdb=" O VAL A 408 " model vdw 2.321 2.440 ... (remaining 61709 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.009 0.069 7466 Z= 0.572 Angle : 1.180 9.151 10090 Z= 0.854 Chirality : 0.076 0.257 1076 Planarity : 0.007 0.122 1288 Dihedral : 15.285 74.466 2785 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 2.16 % Allowed : 17.15 % Favored : 80.69 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 886 helix: -0.42 (0.28), residues: 307 sheet: -1.11 (0.39), residues: 171 loop : -1.14 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 370 HIS 0.003 0.001 HIS B 326 PHE 0.022 0.002 PHE B 373 TYR 0.021 0.002 TYR B 472 ARG 0.008 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8138 (m-10) cc_final: 0.7779 (p90) REVERT: B 87 ASP cc_start: 0.8225 (t0) cc_final: 0.7190 (t70) REVERT: B 89 ASP cc_start: 0.7473 (m-30) cc_final: 0.6974 (m-30) REVERT: B 135 LYS cc_start: 0.7348 (mttt) cc_final: 0.7081 (pptt) REVERT: B 225 ARG cc_start: 0.7472 (mtp180) cc_final: 0.7137 (mtp180) REVERT: A 44 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.6240 (p0) REVERT: A 54 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7428 (ptp-110) REVERT: A 84 VAL cc_start: 0.8370 (t) cc_final: 0.8097 (p) REVERT: A 90 ASP cc_start: 0.7941 (t0) cc_final: 0.7270 (t0) REVERT: A 91 ASP cc_start: 0.8109 (m-30) cc_final: 0.7782 (t70) REVERT: A 263 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7117 (tmm-80) REVERT: A 267 GLN cc_start: 0.8385 (mm110) cc_final: 0.7828 (mp10) outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 1.0247 time to fit residues: 171.0521 Evaluate side-chains 101 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 255 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS B 439 ASN A 15 ASN A 155 GLN A 434 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7466 Z= 0.234 Angle : 0.595 7.050 10090 Z= 0.309 Chirality : 0.043 0.224 1076 Planarity : 0.004 0.037 1288 Dihedral : 5.634 52.207 971 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.68 % Allowed : 19.44 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.24 (0.28), residues: 886 helix: 0.89 (0.28), residues: 323 sheet: -0.88 (0.39), residues: 163 loop : -0.62 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 370 HIS 0.003 0.001 HIS A 320 PHE 0.016 0.002 PHE A 259 TYR 0.014 0.001 TYR B 285 ARG 0.006 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8229 (m-10) cc_final: 0.7826 (p90) REVERT: B 135 LYS cc_start: 0.7629 (mttt) cc_final: 0.7358 (pptt) REVERT: B 148 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: B 400 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6742 (mp0) REVERT: B 471 ILE cc_start: 0.8226 (mt) cc_final: 0.7892 (mp) REVERT: A 41 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.5319 (ptmm) REVERT: A 54 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7549 (ptp-110) REVERT: A 88 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8464 (mm) REVERT: A 91 ASP cc_start: 0.8593 (m-30) cc_final: 0.8192 (t0) outliers start: 29 outliers final: 12 residues processed: 116 average time/residue: 1.0170 time to fit residues: 125.9743 Evaluate side-chains 94 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.0060 chunk 64 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7466 Z= 0.262 Angle : 0.573 5.689 10090 Z= 0.298 Chirality : 0.042 0.232 1076 Planarity : 0.004 0.053 1288 Dihedral : 4.856 37.225 960 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.43 % Allowed : 20.84 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.02 (0.28), residues: 886 helix: 1.12 (0.28), residues: 323 sheet: -0.82 (0.39), residues: 163 loop : -0.43 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 370 HIS 0.003 0.001 HIS A 320 PHE 0.014 0.002 PHE A 158 TYR 0.014 0.001 TYR B 285 ARG 0.008 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8242 (m-10) cc_final: 0.7823 (p90) REVERT: B 135 LYS cc_start: 0.7826 (mttt) cc_final: 0.7375 (pptt) REVERT: B 400 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6875 (mp0) REVERT: B 471 ILE cc_start: 0.8271 (mt) cc_final: 0.7946 (mp) REVERT: A 54 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7582 (ptp-110) REVERT: A 88 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 398 GLU cc_start: 0.8526 (mp0) cc_final: 0.7904 (tm-30) outliers start: 27 outliers final: 14 residues processed: 105 average time/residue: 0.9276 time to fit residues: 104.6251 Evaluate side-chains 100 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7466 Z= 0.314 Angle : 0.595 7.420 10090 Z= 0.305 Chirality : 0.043 0.235 1076 Planarity : 0.004 0.036 1288 Dihedral : 4.953 40.798 959 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.45 % Allowed : 20.08 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.09 (0.28), residues: 886 helix: 1.08 (0.27), residues: 322 sheet: -0.72 (0.38), residues: 165 loop : -0.33 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 370 HIS 0.003 0.001 HIS A 320 PHE 0.014 0.002 PHE A 158 TYR 0.013 0.001 TYR B 285 ARG 0.006 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8243 (m-10) cc_final: 0.7853 (p90) REVERT: B 135 LYS cc_start: 0.7800 (mttt) cc_final: 0.7232 (pptt) REVERT: B 148 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: B 303 MET cc_start: 0.8966 (ttp) cc_final: 0.8747 (ttp) REVERT: B 400 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7166 (mp0) REVERT: B 471 ILE cc_start: 0.8338 (mt) cc_final: 0.8016 (mp) REVERT: A 5 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 41 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.4952 (mtmm) REVERT: A 54 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7684 (ptp-110) REVERT: A 88 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 91 ASP cc_start: 0.8635 (m-30) cc_final: 0.8360 (t0) REVERT: A 212 ASN cc_start: 0.8842 (t0) cc_final: 0.8288 (t0) REVERT: A 255 PHE cc_start: 0.7685 (t80) cc_final: 0.7387 (t80) REVERT: A 267 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8082 (mm-40) REVERT: A 398 GLU cc_start: 0.8514 (mp0) cc_final: 0.7835 (tm-30) outliers start: 35 outliers final: 16 residues processed: 114 average time/residue: 0.9181 time to fit residues: 112.5478 Evaluate side-chains 102 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7466 Z= 0.239 Angle : 0.557 7.091 10090 Z= 0.286 Chirality : 0.042 0.258 1076 Planarity : 0.004 0.062 1288 Dihedral : 4.857 42.095 959 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.57 % Allowed : 20.97 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.29 (0.28), residues: 886 helix: 1.24 (0.28), residues: 324 sheet: -0.60 (0.39), residues: 166 loop : -0.21 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 370 HIS 0.002 0.001 HIS A 320 PHE 0.012 0.001 PHE A 158 TYR 0.011 0.001 TYR B 285 ARG 0.004 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8253 (m-10) cc_final: 0.7875 (p90) REVERT: B 59 HIS cc_start: 0.8342 (t-90) cc_final: 0.8130 (t70) REVERT: B 148 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: B 330 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6859 (pp) REVERT: B 400 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7131 (mp0) REVERT: B 471 ILE cc_start: 0.8360 (mt) cc_final: 0.8032 (mp) REVERT: B 488 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7925 (tt0) REVERT: A 5 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 41 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.5060 (mtmm) REVERT: A 54 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7596 (ptp-110) REVERT: A 77 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: A 88 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 91 ASP cc_start: 0.8624 (m-30) cc_final: 0.8375 (t0) REVERT: A 212 ASN cc_start: 0.8864 (t0) cc_final: 0.8288 (t0) REVERT: A 267 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: A 349 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: A 398 GLU cc_start: 0.8688 (mp0) cc_final: 0.7808 (tm-30) outliers start: 36 outliers final: 14 residues processed: 116 average time/residue: 0.8787 time to fit residues: 109.6997 Evaluate side-chains 107 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7466 Z= 0.257 Angle : 0.569 7.810 10090 Z= 0.292 Chirality : 0.042 0.250 1076 Planarity : 0.004 0.064 1288 Dihedral : 4.880 43.362 959 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.70 % Allowed : 21.35 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.32 (0.28), residues: 886 helix: 1.25 (0.28), residues: 323 sheet: -0.55 (0.39), residues: 166 loop : -0.19 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 370 HIS 0.002 0.001 HIS A 320 PHE 0.015 0.002 PHE A 255 TYR 0.011 0.001 TYR B 285 ARG 0.006 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8261 (m-10) cc_final: 0.7888 (p90) REVERT: B 59 HIS cc_start: 0.8358 (t-90) cc_final: 0.8090 (t70) REVERT: B 148 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6248 (m-80) REVERT: B 330 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6959 (pp) REVERT: B 400 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7191 (mp0) REVERT: B 471 ILE cc_start: 0.8376 (mt) cc_final: 0.8041 (mp) REVERT: A 5 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 41 LYS cc_start: 0.5699 (OUTLIER) cc_final: 0.5083 (mtmm) REVERT: A 54 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7533 (ptp-110) REVERT: A 87 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 91 ASP cc_start: 0.8614 (m-30) cc_final: 0.8394 (t0) REVERT: A 212 ASN cc_start: 0.8882 (t0) cc_final: 0.8315 (t0) REVERT: A 267 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8072 (mm-40) REVERT: A 349 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 398 GLU cc_start: 0.8702 (mp0) cc_final: 0.7812 (tm-30) outliers start: 37 outliers final: 15 residues processed: 114 average time/residue: 1.0237 time to fit residues: 125.0438 Evaluate side-chains 107 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7466 Z= 0.279 Angle : 0.593 7.766 10090 Z= 0.301 Chirality : 0.043 0.250 1076 Planarity : 0.004 0.062 1288 Dihedral : 4.863 43.979 959 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.81 % Allowed : 23.00 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.35 (0.28), residues: 886 helix: 1.24 (0.28), residues: 323 sheet: -0.47 (0.40), residues: 166 loop : -0.17 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 370 HIS 0.002 0.001 HIS A 320 PHE 0.016 0.002 PHE A 259 TYR 0.011 0.001 TYR B 285 ARG 0.007 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8278 (m-10) cc_final: 0.7890 (p90) REVERT: B 112 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8287 (ttpp) REVERT: B 148 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6285 (m-80) REVERT: B 330 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6928 (pp) REVERT: B 400 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7233 (mp0) REVERT: B 471 ILE cc_start: 0.8382 (mt) cc_final: 0.8038 (mp) REVERT: B 488 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7730 (tt0) REVERT: A 5 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 41 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.5119 (mtmm) REVERT: A 54 ARG cc_start: 0.7849 (mtm110) cc_final: 0.7521 (ptp-110) REVERT: A 86 LYS cc_start: 0.8789 (tppp) cc_final: 0.8349 (mptt) REVERT: A 87 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 212 ASN cc_start: 0.8883 (t0) cc_final: 0.8321 (t0) REVERT: A 267 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8073 (mm-40) REVERT: A 349 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: A 398 GLU cc_start: 0.8700 (mp0) cc_final: 0.7805 (tm-30) outliers start: 30 outliers final: 16 residues processed: 109 average time/residue: 0.9928 time to fit residues: 116.4471 Evaluate side-chains 106 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7466 Z= 0.221 Angle : 0.584 8.621 10090 Z= 0.296 Chirality : 0.042 0.248 1076 Planarity : 0.004 0.059 1288 Dihedral : 4.757 44.074 959 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.56 % Allowed : 23.76 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.44 (0.29), residues: 886 helix: 1.31 (0.28), residues: 324 sheet: -0.43 (0.40), residues: 166 loop : -0.13 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 370 HIS 0.009 0.001 HIS B 59 PHE 0.017 0.001 PHE A 259 TYR 0.020 0.001 TYR B 48 ARG 0.007 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8280 (m-10) cc_final: 0.7882 (p90) REVERT: B 148 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: B 330 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6949 (pp) REVERT: B 400 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7212 (mp0) REVERT: B 471 ILE cc_start: 0.8393 (mt) cc_final: 0.8045 (mp) REVERT: B 488 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7714 (tt0) REVERT: B 497 LYS cc_start: 0.9222 (tppt) cc_final: 0.8909 (tmmt) REVERT: A 5 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 41 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.5151 (mtmm) REVERT: A 54 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7344 (ptp-110) REVERT: A 86 LYS cc_start: 0.8785 (tppp) cc_final: 0.8310 (mptt) REVERT: A 87 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8578 (tm-30) REVERT: A 212 ASN cc_start: 0.8882 (t0) cc_final: 0.8340 (t0) REVERT: A 267 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8072 (mm-40) REVERT: A 349 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6816 (pm20) outliers start: 28 outliers final: 16 residues processed: 111 average time/residue: 0.9497 time to fit residues: 113.0385 Evaluate side-chains 108 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7466 Z= 0.257 Angle : 0.617 8.872 10090 Z= 0.313 Chirality : 0.043 0.247 1076 Planarity : 0.004 0.057 1288 Dihedral : 4.800 44.649 959 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.43 % Allowed : 25.16 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.39 (0.28), residues: 886 helix: 1.33 (0.28), residues: 317 sheet: -0.47 (0.39), residues: 171 loop : -0.17 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 370 HIS 0.009 0.001 HIS B 59 PHE 0.018 0.002 PHE A 259 TYR 0.011 0.001 TYR B 285 ARG 0.007 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8290 (m-10) cc_final: 0.7880 (p90) REVERT: B 148 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: B 330 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6941 (pp) REVERT: B 400 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7253 (mp0) REVERT: B 471 ILE cc_start: 0.8390 (mt) cc_final: 0.8044 (mp) REVERT: B 488 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7742 (tt0) REVERT: B 497 LYS cc_start: 0.9221 (tppt) cc_final: 0.8918 (tmmt) REVERT: A 5 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 41 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5212 (mtmm) REVERT: A 54 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7350 (ptp-110) REVERT: A 86 LYS cc_start: 0.8791 (tppp) cc_final: 0.8321 (mptt) REVERT: A 87 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 212 ASN cc_start: 0.8873 (t0) cc_final: 0.8360 (t0) REVERT: A 267 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: A 349 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6822 (pm20) outliers start: 27 outliers final: 13 residues processed: 110 average time/residue: 0.9540 time to fit residues: 112.8443 Evaluate side-chains 105 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7466 Z= 0.212 Angle : 0.607 9.391 10090 Z= 0.305 Chirality : 0.043 0.296 1076 Planarity : 0.004 0.051 1288 Dihedral : 4.719 44.430 959 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.29 % Allowed : 26.43 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.44 (0.29), residues: 886 helix: 1.45 (0.28), residues: 318 sheet: -0.60 (0.38), residues: 177 loop : -0.12 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 370 HIS 0.008 0.001 HIS B 59 PHE 0.019 0.001 PHE A 259 TYR 0.025 0.001 TYR B 48 ARG 0.007 0.000 ARG A 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8281 (m-10) cc_final: 0.7880 (p90) REVERT: B 148 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6296 (m-80) REVERT: B 330 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7017 (pp) REVERT: B 400 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7226 (mp0) REVERT: B 471 ILE cc_start: 0.8378 (mt) cc_final: 0.8030 (mp) REVERT: B 497 LYS cc_start: 0.9210 (tppt) cc_final: 0.8925 (tmmt) REVERT: A 5 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 41 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5231 (mtmm) REVERT: A 54 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7269 (ptp-110) REVERT: A 87 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 184 GLU cc_start: 0.7592 (tt0) cc_final: 0.7344 (tm-30) REVERT: A 212 ASN cc_start: 0.8879 (t0) cc_final: 0.8358 (t0) REVERT: A 267 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7810 (mp-120) REVERT: A 349 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6839 (pm20) outliers start: 18 outliers final: 11 residues processed: 106 average time/residue: 0.9549 time to fit residues: 108.6573 Evaluate side-chains 107 residues out of total 787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.117024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088553 restraints weight = 12460.563| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.31 r_work: 0.3200 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7466 Z= 0.306 Angle : 0.651 10.283 10090 Z= 0.328 Chirality : 0.044 0.280 1076 Planarity : 0.004 0.050 1288 Dihedral : 4.847 45.455 959 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.54 % Allowed : 26.81 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.34 (0.28), residues: 886 helix: 1.26 (0.28), residues: 317 sheet: -0.47 (0.39), residues: 171 loop : -0.18 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 33 HIS 0.009 0.001 HIS B 59 PHE 0.018 0.002 PHE A 259 TYR 0.012 0.001 TYR B 285 ARG 0.007 0.001 ARG A 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2825.43 seconds wall clock time: 50 minutes 15.30 seconds (3015.30 seconds total)