Starting phenix.real_space_refine on Mon Mar 11 14:18:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/03_2024/8jkz_36384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/03_2024/8jkz_36384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/03_2024/8jkz_36384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/03_2024/8jkz_36384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/03_2024/8jkz_36384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/03_2024/8jkz_36384_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.027 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 33 5.16 5 C 5404 2.51 5 N 1443 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" 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: 8444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4674 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain: "B" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3726 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 28, 'TRANS': 440} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.58 Number of scatterers: 8444 At special positions: 0 Unit cell: (78.12, 98.28, 122.64, 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 33 16.00 P 2 15.00 O 1562 8.00 N 1443 7.00 C 5404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 12 sheets defined 36.3% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 removed outlier: 3.794A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.916A pdb=" N LYS A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 101 through 111 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 167 through 176 removed outlier: 3.796A pdb=" N LEU A 171 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 199 through 216 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 287 through 297 removed outlier: 4.075A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 456 through 465 removed outlier: 4.850A pdb=" N ASP A 460 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.574A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.834A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.948A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 139 removed outlier: 4.281A pdb=" N GLN B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.545A pdb=" N CYS B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 185 through 188 No H-bonds generated for 'chain 'B' and resid 185 through 188' Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.509A pdb=" N GLY B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 277 through 295 Processing helix chain 'B' and resid 313 through 320 removed outlier: 3.514A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 removed outlier: 3.968A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 4.023A pdb=" N GLN B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 137 through 140 removed outlier: 6.427A pdb=" N ILE A 181 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR A 140 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 183 " --> pdb=" O THR A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 251 through 255 Processing sheet with id= C, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.550A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 490 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.611A pdb=" N CYS A 345 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= F, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.548A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 11 through 13 Processing sheet with id= H, first strand: chain 'B' and resid 19 through 21 removed outlier: 3.748A pdb=" N ARG B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 49 through 51 No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 52 through 55 removed outlier: 7.291A pdb=" N VAL B 145 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N LEU B 55 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 147 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 148 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN B 181 " --> pdb=" O VAL B 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 231 through 233 Processing sheet with id= L, first strand: chain 'B' and resid 265 through 267 280 hydrogen bonds defined for protein. 789 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: 2.19 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1378 1.31 - 1.43: 2382 1.43 - 1.56: 4838 1.56 - 1.68: 8 1.68 - 1.81: 51 Bond restraints: 8657 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.681 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.281 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.274 0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 8652 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.60: 267 106.60 - 113.83: 4773 113.83 - 121.07: 4178 121.07 - 128.30: 2459 128.30 - 135.53: 71 Bond angle restraints: 11748 Sorted by residual: angle pdb=" C ILE A 390 " pdb=" N PHE A 391 " pdb=" CA PHE A 391 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.43 13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C ALA B 9 " pdb=" CA ALA B 9 " pdb=" CB ALA B 9 " ideal model delta sigma weight residual 116.34 110.45 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " pdb=" O5D NAD A 601 " ideal model delta sigma weight residual 98.00 109.75 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1N NAD A 601 " pdb=" PN NAD A 601 " pdb=" O2N NAD A 601 " ideal model delta sigma weight residual 120.02 109.43 10.59 3.00e+00 1.11e-01 1.25e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4401 17.98 - 35.96: 593 35.96 - 53.95: 154 53.95 - 71.93: 32 71.93 - 89.91: 15 Dihedral angle restraints: 5195 sinusoidal: 2120 harmonic: 3075 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N PRO B 47 " pdb=" CA PRO B 47 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N THR A 375 " pdb=" CA THR A 375 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA MET A 132 " pdb=" C MET A 132 " pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1141 0.070 - 0.140: 130 0.140 - 0.210: 8 0.210 - 0.280: 1 0.280 - 0.351: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3B NAD A 601 " pdb=" C2B NAD A 601 " pdb=" C4B NAD A 601 " pdb=" O3B NAD A 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2D NAD A 601 " pdb=" C1D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" O2D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.37 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 1278 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.33e+00 pdb=" NE ARG A 206 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 391 " -0.011 2.00e-02 2.50e+03 1.52e-02 4.06e+00 pdb=" CG PHE A 391 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 391 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 391 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 391 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 391 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 391 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE A 390 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE A 390 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 391 " 0.010 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1206 2.76 - 3.29: 8053 3.29 - 3.83: 13592 3.83 - 4.36: 15608 4.36 - 4.90: 27387 Nonbonded interactions: 65846 Sorted by model distance: nonbonded pdb=" OH TYR B 83 " pdb=" O ASN B 436 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR B 277 " pdb=" OD2 ASP B 321 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.233 2.440 nonbonded pdb=" OE2 GLU B 330 " pdb=" NH1 ARG B 411 " model vdw 2.267 2.520 nonbonded pdb=" ND2 ASN B 389 " pdb=" OE1 GLN B 392 " model vdw 2.267 2.520 ... (remaining 65841 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.320 Find NCS groups from input model: 0.220 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.007 0.288 8657 Z= 0.458 Angle : 0.735 13.209 11748 Z= 0.398 Chirality : 0.045 0.351 1281 Planarity : 0.004 0.084 1505 Dihedral : 17.975 89.910 3219 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.01 % Favored : 89.90 % Rotamer: Outliers : 1.00 % Allowed : 26.00 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.27), residues: 1049 helix: 0.80 (0.27), residues: 388 sheet: -0.76 (0.40), residues: 189 loop : -2.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.007 0.001 HIS A 52 PHE 0.035 0.002 PHE A 391 TYR 0.013 0.001 TYR B 149 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.2728 time to fit residues: 33.5481 Evaluate side-chains 78 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 257 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0050 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS A 397 ASN B 306 HIS B 317 GLN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8657 Z= 0.178 Angle : 0.538 8.260 11748 Z= 0.280 Chirality : 0.040 0.146 1281 Planarity : 0.004 0.037 1505 Dihedral : 6.685 61.598 1212 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.30 % Favored : 89.61 % Rotamer: Outliers : 4.20 % Allowed : 24.12 % Favored : 71.68 % 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: -1.07 (0.27), residues: 1049 helix: 0.99 (0.28), residues: 383 sheet: -0.75 (0.39), residues: 190 loop : -2.19 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.030 0.001 PHE A 391 TYR 0.013 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 81 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7215 (t80) REVERT: B 49 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7529 (mm-40) REVERT: B 98 LEU cc_start: 0.8922 (tt) cc_final: 0.8473 (tt) REVERT: B 188 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8414 (mt) outliers start: 38 outliers final: 12 residues processed: 113 average time/residue: 0.2187 time to fit residues: 34.2764 Evaluate side-chains 86 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8657 Z= 0.215 Angle : 0.545 7.955 11748 Z= 0.283 Chirality : 0.041 0.145 1281 Planarity : 0.004 0.035 1505 Dihedral : 6.253 56.432 1209 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.68 % Favored : 89.23 % Rotamer: Outliers : 4.65 % Allowed : 24.45 % Favored : 70.91 % 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: -1.03 (0.27), residues: 1049 helix: 1.01 (0.28), residues: 384 sheet: -0.72 (0.39), residues: 190 loop : -2.15 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.013 0.001 PHE B 304 TYR 0.013 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: A 93 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 112 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.4091 (tt) REVERT: B 98 LEU cc_start: 0.8951 (tt) cc_final: 0.8551 (tt) REVERT: B 197 MET cc_start: 0.9049 (mmp) cc_final: 0.8743 (mmm) outliers start: 42 outliers final: 22 residues processed: 115 average time/residue: 0.2160 time to fit residues: 34.6557 Evaluate side-chains 93 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 45 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8657 Z= 0.195 Angle : 0.534 8.324 11748 Z= 0.276 Chirality : 0.041 0.163 1281 Planarity : 0.003 0.035 1505 Dihedral : 6.129 54.681 1209 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.39 % Favored : 89.51 % Rotamer: Outliers : 4.20 % Allowed : 25.22 % Favored : 70.58 % 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: -0.94 (0.27), residues: 1049 helix: 1.13 (0.28), residues: 382 sheet: -0.62 (0.40), residues: 186 loop : -2.14 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.007 0.001 HIS A 52 PHE 0.053 0.001 PHE A 391 TYR 0.012 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 77 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: A 93 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 112 LEU cc_start: 0.4308 (OUTLIER) cc_final: 0.3939 (tt) REVERT: B 188 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8413 (mt) REVERT: B 197 MET cc_start: 0.9033 (mmp) cc_final: 0.8794 (mmm) outliers start: 38 outliers final: 25 residues processed: 109 average time/residue: 0.2170 time to fit residues: 32.8974 Evaluate side-chains 96 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8657 Z= 0.258 Angle : 0.561 7.366 11748 Z= 0.292 Chirality : 0.042 0.188 1281 Planarity : 0.004 0.035 1505 Dihedral : 6.283 58.832 1209 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.68 % Favored : 89.13 % Rotamer: Outliers : 4.65 % Allowed : 25.55 % Favored : 69.80 % 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: -1.00 (0.27), residues: 1049 helix: 1.05 (0.28), residues: 376 sheet: -0.76 (0.39), residues: 191 loop : -2.08 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.008 0.001 HIS A 52 PHE 0.016 0.002 PHE A 9 TYR 0.014 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 76 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: A 93 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7337 (t80) REVERT: A 112 LEU cc_start: 0.4375 (OUTLIER) cc_final: 0.4010 (tt) REVERT: A 132 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8331 (ptm) REVERT: A 372 LEU cc_start: 0.8802 (mt) cc_final: 0.8407 (mp) REVERT: A 403 TYR cc_start: 0.7049 (m-80) cc_final: 0.6841 (m-80) REVERT: A 496 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6709 (tp30) REVERT: B 188 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 397 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7972 (mt-10) outliers start: 42 outliers final: 27 residues processed: 110 average time/residue: 0.2075 time to fit residues: 32.4374 Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 71 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 473 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8657 Z= 0.163 Angle : 0.528 7.919 11748 Z= 0.272 Chirality : 0.040 0.155 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.983 57.350 1207 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.91 % Favored : 89.90 % Rotamer: Outliers : 3.98 % Allowed : 26.66 % Favored : 69.36 % 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: -0.90 (0.27), residues: 1049 helix: 1.12 (0.28), residues: 377 sheet: -0.63 (0.40), residues: 187 loop : -2.04 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.011 0.001 PHE A 328 TYR 0.012 0.001 TYR B 366 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 112 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3973 (tt) REVERT: A 132 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (ptm) REVERT: A 372 LEU cc_start: 0.8822 (mt) cc_final: 0.8412 (mp) REVERT: A 403 TYR cc_start: 0.7072 (m-80) cc_final: 0.6856 (m-80) REVERT: A 496 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: B 146 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8226 (tt) REVERT: B 397 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7866 (mt-10) outliers start: 36 outliers final: 22 residues processed: 112 average time/residue: 0.2018 time to fit residues: 31.7765 Evaluate side-chains 103 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 61 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8657 Z= 0.173 Angle : 0.534 7.819 11748 Z= 0.273 Chirality : 0.040 0.152 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.940 55.528 1207 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.58 % Favored : 89.32 % Rotamer: Outliers : 4.31 % Allowed : 26.22 % Favored : 69.47 % 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: -0.87 (0.27), residues: 1049 helix: 1.16 (0.28), residues: 377 sheet: -0.62 (0.40), residues: 187 loop : -2.02 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.036 0.001 PHE A 391 TYR 0.012 0.001 TYR A 101 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 75 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7369 (t80) REVERT: A 112 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4155 (tt) REVERT: A 132 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8301 (ptm) REVERT: A 372 LEU cc_start: 0.8791 (mt) cc_final: 0.8387 (mp) REVERT: A 403 TYR cc_start: 0.7052 (m-80) cc_final: 0.6799 (m-80) REVERT: A 496 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: B 146 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8271 (tt) REVERT: B 397 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7854 (mt-10) outliers start: 39 outliers final: 26 residues processed: 109 average time/residue: 0.2003 time to fit residues: 30.9771 Evaluate side-chains 101 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 238 GLN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8657 Z= 0.177 Angle : 0.533 8.017 11748 Z= 0.274 Chirality : 0.040 0.167 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.927 54.158 1207 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.49 % Favored : 89.42 % Rotamer: Outliers : 4.31 % Allowed : 26.22 % Favored : 69.47 % 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: -0.89 (0.27), residues: 1049 helix: 1.09 (0.28), residues: 377 sheet: -0.62 (0.40), residues: 187 loop : -2.00 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.026 0.001 PHE B 163 TYR 0.011 0.001 TYR B 366 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 77 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 132 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8306 (ptm) REVERT: A 372 LEU cc_start: 0.8789 (mt) cc_final: 0.8387 (mp) REVERT: A 403 TYR cc_start: 0.7035 (m-80) cc_final: 0.6772 (m-80) REVERT: A 496 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6583 (tp30) REVERT: B 146 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8246 (tt) REVERT: B 397 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7827 (mt-10) outliers start: 39 outliers final: 28 residues processed: 110 average time/residue: 0.1879 time to fit residues: 29.7804 Evaluate side-chains 106 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 93 optimal weight: 0.0000 chunk 61 optimal weight: 0.5980 chunk 98 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 overall best weight: 0.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS A 397 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8657 Z= 0.137 Angle : 0.519 7.844 11748 Z= 0.264 Chirality : 0.039 0.156 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.596 52.730 1207 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.96 % Favored : 90.94 % Rotamer: Outliers : 2.77 % Allowed : 27.54 % Favored : 69.69 % 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: -0.81 (0.27), residues: 1049 helix: 1.08 (0.28), residues: 385 sheet: -0.40 (0.40), residues: 187 loop : -2.01 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 340 HIS 0.005 0.001 HIS A 46 PHE 0.041 0.001 PHE A 391 TYR 0.013 0.001 TYR A 101 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 112 LEU cc_start: 0.4644 (OUTLIER) cc_final: 0.4248 (tt) REVERT: A 132 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8208 (ptm) REVERT: A 403 TYR cc_start: 0.7067 (m-80) cc_final: 0.6703 (m-80) REVERT: B 133 MET cc_start: 0.8333 (tpt) cc_final: 0.7541 (mmm) outliers start: 25 outliers final: 17 residues processed: 111 average time/residue: 0.2040 time to fit residues: 32.1597 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0570 chunk 68 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 63 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8657 Z= 0.138 Angle : 0.532 8.321 11748 Z= 0.271 Chirality : 0.040 0.166 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.505 52.666 1207 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.06 % Favored : 90.85 % Rotamer: Outliers : 2.43 % Allowed : 27.77 % Favored : 69.80 % 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: -0.71 (0.27), residues: 1049 helix: 1.16 (0.28), residues: 384 sheet: -0.13 (0.41), residues: 176 loop : -2.02 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 340 HIS 0.004 0.001 HIS A 46 PHE 0.044 0.001 PHE B 137 TYR 0.009 0.001 TYR B 366 ARG 0.006 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7373 (t80) REVERT: A 112 LEU cc_start: 0.4822 (OUTLIER) cc_final: 0.4454 (tt) REVERT: A 132 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8157 (ptm) REVERT: A 403 TYR cc_start: 0.7193 (m-80) cc_final: 0.6915 (m-80) REVERT: B 49 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7321 (mm-40) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.2009 time to fit residues: 28.8639 Evaluate side-chains 93 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.157914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118359 restraints weight = 11806.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115603 restraints weight = 11971.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116864 restraints weight = 14537.694| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8657 Z= 0.153 Angle : 0.544 7.769 11748 Z= 0.275 Chirality : 0.040 0.156 1281 Planarity : 0.003 0.035 1505 Dihedral : 5.531 53.127 1207 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.44 % Favored : 90.47 % Rotamer: Outliers : 2.32 % Allowed : 28.10 % Favored : 69.58 % 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: -0.72 (0.27), residues: 1049 helix: 1.19 (0.28), residues: 384 sheet: -0.33 (0.40), residues: 186 loop : -2.01 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 377 HIS 0.004 0.001 HIS A 52 PHE 0.072 0.001 PHE B 137 TYR 0.014 0.001 TYR A 101 ARG 0.006 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.97 seconds wall clock time: 33 minutes 18.31 seconds (1998.31 seconds total)