Starting phenix.real_space_refine on Fri Jul 19 09:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k34_36843/07_2024/8k34_36843_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k34_36843/07_2024/8k34_36843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k34_36843/07_2024/8k34_36843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k34_36843/07_2024/8k34_36843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k34_36843/07_2024/8k34_36843_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k34_36843/07_2024/8k34_36843_neut.cif" } resolution = 2.81 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 4650 2.51 5 N 1196 2.21 5 O 1315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A ASP 387": "OD1" <-> "OD2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7187 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3597 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 13, 'TRANS': 415} Chain breaks: 4 Chain: "B" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3503 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 409} Chain breaks: 3 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.26, per 1000 atoms: 0.59 Number of scatterers: 7187 At special positions: 0 Unit cell: (75.9, 81.4, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 4 15.00 Mg 1 11.99 O 1315 8.00 N 1196 7.00 C 4650 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: 4.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.544A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.113A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.805A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.690A pdb=" N PHE A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.587A pdb=" N ARG A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) 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 365 removed outlier: 3.724A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'A' and resid 420 through 438 removed outlier: 3.824A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) 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 62 removed outlier: 3.744A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 115 through 132 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.860A pdb=" N LYS B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.699A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.596A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 4.043A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 5.832A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 4 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 8 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 394 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 6 removed outlier: 5.712A pdb=" N ILE B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE B 419 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.775A pdb=" N GLN B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.608A pdb=" N GLY B 45 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB3, first strand: chain 'B' and resid 425 through 426 293 hydrogen bonds defined for protein. 816 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: 2.17 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2203 1.34 - 1.46: 1336 1.46 - 1.58: 3792 1.58 - 1.70: 7 1.70 - 1.82: 31 Bond restraints: 7369 Sorted by residual: bond pdb=" CG PRO B 319 " pdb=" CD PRO B 319 " ideal model delta sigma weight residual 1.503 1.384 0.119 3.40e-02 8.65e+02 1.22e+01 bond pdb=" CG LEU B 13 " pdb=" CD1 LEU B 13 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.28e+00 bond pdb=" CG LYS B 48 " pdb=" CD LYS B 48 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CG LEU B 57 " pdb=" CD2 LEU B 57 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 ... (remaining 7364 not shown) Histogram of bond angle deviations from ideal: 93.83 - 101.90: 17 101.90 - 109.97: 1096 109.97 - 118.04: 4422 118.04 - 126.11: 4280 126.11 - 134.18: 150 Bond angle restraints: 9965 Sorted by residual: angle pdb=" CA LYS A 315 " pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " ideal model delta sigma weight residual 114.10 127.02 -12.92 2.00e+00 2.50e-01 4.17e+01 angle pdb=" CA PRO B 319 " pdb=" N PRO B 319 " pdb=" CD PRO B 319 " ideal model delta sigma weight residual 112.00 103.09 8.91 1.40e+00 5.10e-01 4.05e+01 angle pdb=" N PRO B 319 " pdb=" CD PRO B 319 " pdb=" CG PRO B 319 " ideal model delta sigma weight residual 103.20 93.83 9.37 1.50e+00 4.44e-01 3.90e+01 angle pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " pdb=" CD LYS B 48 " ideal model delta sigma weight residual 111.30 121.94 -10.64 2.30e+00 1.89e-01 2.14e+01 angle pdb=" CA GLN B 295 " pdb=" CB GLN B 295 " pdb=" CG GLN B 295 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 ... (remaining 9960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3676 16.42 - 32.83: 503 32.83 - 49.25: 169 49.25 - 65.67: 49 65.67 - 82.09: 10 Dihedral angle restraints: 4407 sinusoidal: 1875 harmonic: 2532 Sorted by residual: dihedral pdb=" CA PRO B 393 " pdb=" C PRO B 393 " pdb=" N LEU B 394 " pdb=" CA LEU B 394 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA SER A 173 " pdb=" C SER A 173 " pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR A 216 " pdb=" C THR A 216 " pdb=" N PHE A 217 " pdb=" CA PHE A 217 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 640 0.031 - 0.062: 286 0.062 - 0.093: 87 0.093 - 0.124: 50 0.124 - 0.155: 13 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA LEU B 57 " pdb=" N LEU B 57 " pdb=" C LEU B 57 " pdb=" CB LEU B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CB ILE B 486 " pdb=" CA ILE B 486 " pdb=" CG1 ILE B 486 " pdb=" CG2 ILE B 486 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE A 391 " pdb=" N ILE A 391 " pdb=" C ILE A 391 " pdb=" CB ILE A 391 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1073 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 318 " 0.079 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 319 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 295 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C GLN B 295 " 0.037 2.00e-02 2.50e+03 pdb=" O GLN B 295 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 296 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 394 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ASN A 394 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 394 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 395 " -0.012 2.00e-02 2.50e+03 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 80 2.58 - 3.16: 5839 3.16 - 3.74: 11725 3.74 - 4.32: 16273 4.32 - 4.90: 26684 Nonbonded interactions: 60601 Sorted by model distance: nonbonded pdb=" OD1 ASN B 468 " pdb="MG MG B 601 " model vdw 2.000 2.170 nonbonded pdb=" OP1 A C 3 " pdb="MG MG B 601 " model vdw 2.008 2.170 nonbonded pdb=" OP2 A C 1 " pdb="MG MG B 601 " model vdw 2.023 2.170 nonbonded pdb=" OXT ILE B 507 " pdb="MG MG B 601 " model vdw 2.088 2.170 nonbonded pdb=" O TRP B 269 " pdb=" OH TYR B 467 " model vdw 2.144 2.440 ... (remaining 60596 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: 1.270 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.560 Find NCS groups from input model: 0.100 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:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 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 : 0.004 0.119 7369 Z= 0.275 Angle : 0.737 12.915 9965 Z= 0.396 Chirality : 0.044 0.155 1076 Planarity : 0.005 0.113 1242 Dihedral : 17.750 82.086 2767 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.07 % Allowed : 31.05 % Favored : 66.88 % 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: -0.23 (0.28), residues: 845 helix: 0.61 (0.31), residues: 280 sheet: -0.17 (0.41), residues: 153 loop : -0.60 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 46 HIS 0.005 0.001 HIS A 358 PHE 0.027 0.002 PHE A 305 TYR 0.021 0.001 TYR B 506 ARG 0.008 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.6775 (mp10) cc_final: 0.6572 (mp10) REVERT: A 346 ASP cc_start: 0.7995 (m-30) cc_final: 0.7732 (m-30) REVERT: B 356 GLU cc_start: 0.7885 (mp0) cc_final: 0.7657 (mp0) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.7274 time to fit residues: 89.0877 Evaluate side-chains 102 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 311 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 434 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7369 Z= 0.254 Angle : 0.592 7.132 9965 Z= 0.310 Chirality : 0.044 0.139 1076 Planarity : 0.004 0.060 1242 Dihedral : 8.228 75.653 993 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.47 % Allowed : 24.19 % Favored : 69.34 % 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: -0.15 (0.28), residues: 845 helix: 0.68 (0.30), residues: 293 sheet: -0.09 (0.42), residues: 149 loop : -0.60 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 46 HIS 0.004 0.001 HIS A 320 PHE 0.027 0.002 PHE A 343 TYR 0.011 0.001 TYR B 506 ARG 0.006 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 102 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7963 (m) cc_final: 0.7563 (m) REVERT: A 89 GLN cc_start: 0.8016 (mp10) cc_final: 0.7799 (pm20) REVERT: A 119 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7874 (p0) REVERT: A 189 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5979 (tpm170) REVERT: A 346 ASP cc_start: 0.7990 (m-30) cc_final: 0.7675 (m-30) REVERT: A 371 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.6120 (m-30) REVERT: A 394 ASN cc_start: 0.5450 (OUTLIER) cc_final: 0.5113 (p0) outliers start: 50 outliers final: 18 residues processed: 135 average time/residue: 0.8300 time to fit residues: 120.9058 Evaluate side-chains 113 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7369 Z= 0.206 Angle : 0.561 7.525 9965 Z= 0.295 Chirality : 0.043 0.163 1076 Planarity : 0.004 0.047 1242 Dihedral : 7.749 75.581 983 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.30 % Allowed : 26.65 % Favored : 68.05 % 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: -0.11 (0.28), residues: 845 helix: 0.85 (0.30), residues: 292 sheet: -0.05 (0.42), residues: 140 loop : -0.69 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 370 HIS 0.004 0.001 HIS A 320 PHE 0.023 0.001 PHE A 343 TYR 0.012 0.001 TYR A 190 ARG 0.007 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 105 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7842 (m) cc_final: 0.7464 (m) REVERT: A 31 GLU cc_start: 0.6723 (tp30) cc_final: 0.6432 (tp30) REVERT: A 41 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5695 (pptt) REVERT: A 89 GLN cc_start: 0.8057 (mp10) cc_final: 0.7829 (pm20) REVERT: A 346 ASP cc_start: 0.7992 (m-30) cc_final: 0.7654 (m-30) REVERT: A 371 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6097 (m-30) REVERT: B 350 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7448 (t0) REVERT: B 371 ASN cc_start: 0.6954 (m110) cc_final: 0.6688 (m-40) REVERT: B 474 ASP cc_start: 0.7081 (t0) cc_final: 0.6827 (t0) outliers start: 41 outliers final: 18 residues processed: 130 average time/residue: 0.7756 time to fit residues: 109.4253 Evaluate side-chains 117 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7369 Z= 0.174 Angle : 0.539 7.486 9965 Z= 0.281 Chirality : 0.042 0.150 1076 Planarity : 0.004 0.043 1242 Dihedral : 7.600 75.038 983 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.17 % Allowed : 26.65 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 845 helix: 1.03 (0.31), residues: 292 sheet: -0.16 (0.42), residues: 154 loop : -0.61 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 370 HIS 0.004 0.001 HIS A 320 PHE 0.021 0.001 PHE A 305 TYR 0.011 0.001 TYR A 190 ARG 0.006 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7913 (m) cc_final: 0.7560 (m) REVERT: A 41 LYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5522 (pptt) REVERT: A 89 GLN cc_start: 0.8107 (mp10) cc_final: 0.7863 (pm20) REVERT: A 108 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 346 ASP cc_start: 0.7956 (m-30) cc_final: 0.7635 (m-30) REVERT: A 371 ASP cc_start: 0.6254 (OUTLIER) cc_final: 0.5985 (m-30) REVERT: B 286 LYS cc_start: 0.7982 (tppt) cc_final: 0.7423 (mptt) REVERT: B 302 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: B 305 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7543 (mm) REVERT: B 367 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 371 ASN cc_start: 0.6853 (m110) cc_final: 0.6418 (m-40) REVERT: B 453 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6989 (mp10) outliers start: 40 outliers final: 16 residues processed: 130 average time/residue: 0.6955 time to fit residues: 99.1146 Evaluate side-chains 117 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7369 Z= 0.196 Angle : 0.537 7.827 9965 Z= 0.280 Chirality : 0.042 0.147 1076 Planarity : 0.004 0.047 1242 Dihedral : 7.355 74.009 980 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.43 % Allowed : 27.30 % Favored : 67.27 % 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: 0.02 (0.28), residues: 845 helix: 1.04 (0.30), residues: 292 sheet: -0.21 (0.41), residues: 156 loop : -0.61 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 368 HIS 0.004 0.001 HIS A 320 PHE 0.021 0.001 PHE A 343 TYR 0.013 0.001 TYR A 190 ARG 0.005 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7950 (m) cc_final: 0.7605 (m) REVERT: A 41 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5584 (pptt) REVERT: A 89 GLN cc_start: 0.8065 (mp10) cc_final: 0.7831 (pm20) REVERT: A 108 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 119 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7808 (p0) REVERT: A 305 PHE cc_start: 0.7630 (t80) cc_final: 0.7374 (t80) REVERT: A 346 ASP cc_start: 0.7964 (m-30) cc_final: 0.7670 (m-30) REVERT: A 358 HIS cc_start: 0.7876 (m-70) cc_final: 0.7613 (m-70) REVERT: A 371 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5900 (m-30) REVERT: B 286 LYS cc_start: 0.7972 (tppt) cc_final: 0.7399 (mptt) REVERT: B 350 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7541 (t0) REVERT: B 371 ASN cc_start: 0.6911 (m110) cc_final: 0.6550 (m-40) REVERT: B 453 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6969 (mp10) outliers start: 42 outliers final: 22 residues processed: 128 average time/residue: 0.7681 time to fit residues: 106.9625 Evaluate side-chains 125 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7369 Z= 0.216 Angle : 0.568 8.187 9965 Z= 0.296 Chirality : 0.043 0.141 1076 Planarity : 0.004 0.057 1242 Dihedral : 7.397 73.581 980 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.43 % Allowed : 27.43 % Favored : 67.14 % 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: -0.04 (0.28), residues: 845 helix: 1.04 (0.31), residues: 292 sheet: -0.31 (0.41), residues: 156 loop : -0.65 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.022 0.002 PHE A 343 TYR 0.014 0.001 TYR A 190 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7954 (m) cc_final: 0.7613 (m) REVERT: A 41 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5594 (pptt) REVERT: A 108 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 119 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7838 (p0) REVERT: A 281 ASN cc_start: 0.8265 (t0) cc_final: 0.8064 (p0) REVERT: A 305 PHE cc_start: 0.7656 (t80) cc_final: 0.7415 (t80) REVERT: A 346 ASP cc_start: 0.8020 (m-30) cc_final: 0.7787 (m-30) REVERT: A 371 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5938 (m-30) REVERT: B 302 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.5859 (mp-120) REVERT: B 371 ASN cc_start: 0.6845 (m110) cc_final: 0.6366 (m-40) REVERT: B 453 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7045 (mp10) outliers start: 42 outliers final: 22 residues processed: 132 average time/residue: 0.7001 time to fit residues: 100.8775 Evaluate side-chains 124 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7369 Z= 0.202 Angle : 0.571 7.832 9965 Z= 0.296 Chirality : 0.042 0.138 1076 Planarity : 0.004 0.049 1242 Dihedral : 7.358 73.565 980 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.92 % Allowed : 28.33 % Favored : 66.75 % 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: 0.03 (0.28), residues: 845 helix: 1.11 (0.31), residues: 292 sheet: -0.19 (0.41), residues: 149 loop : -0.66 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.021 0.001 PHE A 343 TYR 0.014 0.001 TYR B 506 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7975 (m) cc_final: 0.7637 (m) REVERT: A 41 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5612 (pptt) REVERT: A 108 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 277 MET cc_start: 0.7170 (mmp) cc_final: 0.6845 (mmp) REVERT: A 305 PHE cc_start: 0.7707 (t80) cc_final: 0.7493 (t80) REVERT: A 346 ASP cc_start: 0.7959 (m-30) cc_final: 0.7664 (m-30) REVERT: A 358 HIS cc_start: 0.7801 (m-70) cc_final: 0.7570 (m-70) REVERT: A 371 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5911 (m-30) REVERT: B 229 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6917 (mt) REVERT: B 305 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7617 (mm) REVERT: B 350 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7693 (t0) REVERT: B 371 ASN cc_start: 0.7068 (m110) cc_final: 0.6705 (m110) REVERT: B 453 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7037 (mp10) outliers start: 38 outliers final: 20 residues processed: 126 average time/residue: 0.7582 time to fit residues: 104.2617 Evaluate side-chains 122 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7369 Z= 0.306 Angle : 0.649 9.462 9965 Z= 0.336 Chirality : 0.045 0.155 1076 Planarity : 0.004 0.053 1242 Dihedral : 7.655 73.662 980 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.69 % Allowed : 27.81 % Favored : 66.49 % 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: -0.25 (0.28), residues: 845 helix: 0.81 (0.30), residues: 291 sheet: -0.41 (0.41), residues: 156 loop : -0.72 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 369 HIS 0.004 0.001 HIS A 358 PHE 0.029 0.002 PHE A 343 TYR 0.022 0.002 TYR B 506 ARG 0.006 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 106 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7968 (m) cc_final: 0.7622 (m) REVERT: A 41 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5754 (pptt) REVERT: A 99 ILE cc_start: 0.7478 (pt) cc_final: 0.7256 (pt) REVERT: A 108 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 119 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7846 (p0) REVERT: A 277 MET cc_start: 0.7119 (mmp) cc_final: 0.6639 (mmp) REVERT: A 305 PHE cc_start: 0.7684 (t80) cc_final: 0.7406 (t80) REVERT: A 346 ASP cc_start: 0.8052 (m-30) cc_final: 0.7768 (m-30) REVERT: A 358 HIS cc_start: 0.7875 (m-70) cc_final: 0.7653 (m-70) REVERT: A 371 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: B 229 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6885 (mt) REVERT: B 302 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.5862 (mp-120) REVERT: B 350 ASN cc_start: 0.8183 (t0) cc_final: 0.7776 (t0) REVERT: B 453 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6968 (mp10) outliers start: 44 outliers final: 19 residues processed: 131 average time/residue: 0.7447 time to fit residues: 106.1882 Evaluate side-chains 127 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7369 Z= 0.236 Angle : 0.628 11.002 9965 Z= 0.323 Chirality : 0.044 0.140 1076 Planarity : 0.004 0.052 1242 Dihedral : 7.546 73.575 980 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.40 % Allowed : 29.37 % Favored : 66.24 % 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: -0.17 (0.28), residues: 845 helix: 0.93 (0.31), residues: 291 sheet: -0.37 (0.41), residues: 152 loop : -0.73 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.025 0.002 PHE A 343 TYR 0.019 0.002 TYR A 190 ARG 0.006 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7948 (m) cc_final: 0.7609 (m) REVERT: A 41 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5666 (pptt) REVERT: A 108 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 119 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7772 (p0) REVERT: A 277 MET cc_start: 0.7053 (mmp) cc_final: 0.6515 (mmp) REVERT: A 305 PHE cc_start: 0.7681 (t80) cc_final: 0.7408 (t80) REVERT: A 346 ASP cc_start: 0.7997 (m-30) cc_final: 0.7729 (m-30) REVERT: A 358 HIS cc_start: 0.7885 (m-70) cc_final: 0.7650 (m-70) REVERT: A 371 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5921 (m-30) REVERT: B 229 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6857 (mt) REVERT: B 302 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6315 (mp-120) REVERT: B 305 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7639 (mm) REVERT: B 350 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7592 (t0) REVERT: B 371 ASN cc_start: 0.7071 (m110) cc_final: 0.6695 (m110) REVERT: B 453 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: B 474 ASP cc_start: 0.7015 (t0) cc_final: 0.6742 (t0) outliers start: 34 outliers final: 19 residues processed: 125 average time/residue: 0.6826 time to fit residues: 93.7996 Evaluate side-chains 129 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.0670 chunk 71 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7369 Z= 0.204 Angle : 0.628 11.583 9965 Z= 0.323 Chirality : 0.043 0.144 1076 Planarity : 0.004 0.054 1242 Dihedral : 7.473 74.134 980 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.01 % Allowed : 30.40 % Favored : 65.59 % 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: -0.10 (0.28), residues: 845 helix: 1.05 (0.31), residues: 292 sheet: -0.24 (0.43), residues: 145 loop : -0.78 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.023 0.001 PHE A 343 TYR 0.019 0.001 TYR B 506 ARG 0.006 0.000 ARG B 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7922 (m) cc_final: 0.7590 (m) REVERT: A 41 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5793 (pptt) REVERT: A 108 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 277 MET cc_start: 0.7168 (mmp) cc_final: 0.6662 (mmp) REVERT: A 305 PHE cc_start: 0.7679 (t80) cc_final: 0.7409 (t80) REVERT: A 314 GLN cc_start: 0.8309 (tt0) cc_final: 0.8056 (tt0) REVERT: A 346 ASP cc_start: 0.7938 (m-30) cc_final: 0.7688 (m-30) REVERT: A 358 HIS cc_start: 0.7874 (m-70) cc_final: 0.7634 (m-70) REVERT: A 371 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5905 (m-30) REVERT: B 229 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6868 (mt) REVERT: B 305 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7664 (mm) REVERT: B 350 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7581 (t0) REVERT: B 371 ASN cc_start: 0.7126 (m110) cc_final: 0.6758 (m110) REVERT: B 453 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7001 (mp10) outliers start: 31 outliers final: 16 residues processed: 128 average time/residue: 0.7933 time to fit residues: 110.0194 Evaluate side-chains 121 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.177691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.145854 restraints weight = 10251.004| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.46 r_work: 0.4036 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7369 Z= 0.242 Angle : 0.654 10.503 9965 Z= 0.334 Chirality : 0.044 0.143 1076 Planarity : 0.004 0.054 1242 Dihedral : 7.526 73.735 978 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.88 % Allowed : 30.40 % Favored : 65.72 % 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: -0.21 (0.28), residues: 845 helix: 0.93 (0.30), residues: 292 sheet: -0.27 (0.43), residues: 145 loop : -0.83 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.025 0.002 PHE A 343 TYR 0.022 0.001 TYR B 506 ARG 0.006 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.56 seconds wall clock time: 47 minutes 26.70 seconds (2846.70 seconds total)