Starting phenix.real_space_refine on Tue Feb 11 06:16:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryq_24745/02_2025/7ryq_24745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryq_24745/02_2025/7ryq_24745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ryq_24745/02_2025/7ryq_24745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryq_24745/02_2025/7ryq_24745.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryq_24745/02_2025/7ryq_24745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryq_24745/02_2025/7ryq_24745.cif" } resolution = 4.6 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2773 2.51 5 N 744 2.21 5 O 790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4332 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4332 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain breaks: 5 Time building chain proxies: 3.43, per 1000 atoms: 0.79 Number of scatterers: 4332 At special positions: 0 Unit cell: (75.46, 74.48, 142.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 790 8.00 N 744 7.00 C 2773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 477.6 milliseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 5 through 21 removed outlier: 3.993A pdb=" N ALA B 18 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 removed outlier: 3.725A pdb=" N LEU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.730A pdb=" N ALA B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.599A pdb=" N ASN B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.761A pdb=" N ALA B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.856A pdb=" N ASN B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.507A pdb=" N LYS B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 264 removed outlier: 4.241A pdb=" N ASN B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 255 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 removed outlier: 5.374A pdb=" N HIS B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 306 through 325 removed outlier: 3.670A pdb=" N ILE B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 321 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 346 through 364 removed outlier: 3.568A pdb=" N LYS B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 389 through 410 removed outlier: 4.989A pdb=" N VAL B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 434 removed outlier: 3.628A pdb=" N HIS B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 460 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 464 through 492 Processing helix chain 'B' and resid 500 through 525 Processing helix chain 'B' and resid 539 through 555 Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.923A pdb=" N GLU B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 566 " --> pdb=" O PRO B 562 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 621 Proline residue: B 608 - end of helix 274 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.20 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: 1400 1.34 - 1.46: 788 1.46 - 1.58: 2192 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 4419 Sorted by residual: bond pdb=" CA ARG B 385 " pdb=" CB ARG B 385 " ideal model delta sigma weight residual 1.526 1.545 -0.019 9.30e-03 1.16e+04 4.16e+00 bond pdb=" N GLU B 109 " pdb=" CA GLU B 109 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.32e-02 5.74e+03 2.75e+00 bond pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 1.517 1.538 -0.021 1.46e-02 4.69e+03 2.10e+00 bond pdb=" CA PHE B 203 " pdb=" CB PHE B 203 " ideal model delta sigma weight residual 1.528 1.550 -0.022 1.56e-02 4.11e+03 1.90e+00 bond pdb=" CA LEU B 111 " pdb=" C LEU B 111 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.12e-02 7.97e+03 1.88e+00 ... (remaining 4414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 5786 2.87 - 5.74: 148 5.74 - 8.62: 14 8.62 - 11.49: 1 11.49 - 14.36: 2 Bond angle restraints: 5951 Sorted by residual: angle pdb=" N ASN B 528 " pdb=" CA ASN B 528 " pdb=" C ASN B 528 " ideal model delta sigma weight residual 109.41 123.29 -13.88 1.52e+00 4.33e-01 8.34e+01 angle pdb=" N LYS B 205 " pdb=" CA LYS B 205 " pdb=" C LYS B 205 " ideal model delta sigma weight residual 110.80 125.16 -14.36 2.13e+00 2.20e-01 4.55e+01 angle pdb=" N VAL B 381 " pdb=" CA VAL B 381 " pdb=" C VAL B 381 " ideal model delta sigma weight residual 112.98 106.45 6.53 1.25e+00 6.40e-01 2.73e+01 angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 113.53 120.63 -7.10 1.39e+00 5.18e-01 2.61e+01 angle pdb=" N LYS B 350 " pdb=" CA LYS B 350 " pdb=" C LYS B 350 " ideal model delta sigma weight residual 111.28 116.24 -4.96 1.09e+00 8.42e-01 2.07e+01 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2406 17.34 - 34.69: 216 34.69 - 52.03: 61 52.03 - 69.37: 13 69.37 - 86.71: 6 Dihedral angle restraints: 2702 sinusoidal: 1126 harmonic: 1576 Sorted by residual: dihedral pdb=" CA LEU B 94 " pdb=" C LEU B 94 " pdb=" N ALA B 95 " pdb=" CA ALA B 95 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA GLU B 437 " pdb=" C GLU B 437 " pdb=" N THR B 438 " pdb=" CA THR B 438 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP B 388 " pdb=" C ASP B 388 " pdb=" N PHE B 389 " pdb=" CA PHE B 389 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 535 0.068 - 0.135: 96 0.135 - 0.202: 14 0.202 - 0.270: 4 0.270 - 0.337: 3 Chirality restraints: 652 Sorted by residual: chirality pdb=" CA LYS B 205 " pdb=" N LYS B 205 " pdb=" C LYS B 205 " pdb=" CB LYS B 205 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA GLU B 109 " pdb=" N GLU B 109 " pdb=" C GLU B 109 " pdb=" CB GLU B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" C PRO B 527 " pdb=" CB PRO B 527 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 649 not shown) Planarity restraints: 758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 51 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO B 52 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 578 " 0.026 2.00e-02 2.50e+03 2.18e-02 8.28e+00 pdb=" CG PHE B 578 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 578 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 578 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 578 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 578 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 578 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 526 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO B 527 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.036 5.00e-02 4.00e+02 ... (remaining 755 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 7 1.98 - 2.71: 275 2.71 - 3.44: 7338 3.44 - 4.17: 10282 4.17 - 4.90: 17111 Nonbonded interactions: 35013 Sorted by model distance: nonbonded pdb=" CA SER B 523 " pdb=" CG PRO B 527 " model vdw 1.251 3.870 nonbonded pdb=" N SER B 523 " pdb=" CG PRO B 527 " model vdw 1.404 3.520 nonbonded pdb=" O ASP B 522 " pdb=" CD PRO B 527 " model vdw 1.613 3.440 nonbonded pdb=" NE ARG B 525 " pdb=" OE1 GLU B 533 " model vdw 1.718 3.120 nonbonded pdb=" CD ARG B 525 " pdb=" OE1 GLU B 533 " model vdw 1.721 3.440 ... (remaining 35008 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.005 0.048 4419 Z= 0.327 Angle : 1.083 14.362 5951 Z= 0.668 Chirality : 0.058 0.337 652 Planarity : 0.007 0.079 758 Dihedral : 15.485 86.712 1674 Min Nonbonded Distance : 1.251 Molprobity Statistics. All-atom Clashscore : 39.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.68 % Favored : 88.93 % Rotamer: Outliers : 6.25 % Allowed : 3.23 % Favored : 90.52 % 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: -1.51 (0.36), residues: 515 helix: -0.47 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -2.28 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 314 HIS 0.008 0.002 HIS B 447 PHE 0.050 0.004 PHE B 578 TYR 0.026 0.003 TYR B 516 ARG 0.009 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8296 (mm-40) REVERT: B 335 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9039 (mm-30) REVERT: B 397 LEU cc_start: 0.9336 (tt) cc_final: 0.9102 (mt) REVERT: B 486 ASP cc_start: 0.8766 (m-30) cc_final: 0.8514 (m-30) outliers start: 29 outliers final: 12 residues processed: 82 average time/residue: 0.2387 time to fit residues: 23.2364 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 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 = 0.3518 r_free = 0.3518 target = 0.067456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.057844 restraints weight = 45614.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.058858 restraints weight = 29278.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059640 restraints weight = 21145.980| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4419 Z= 0.234 Angle : 0.816 13.926 5951 Z= 0.428 Chirality : 0.048 0.373 652 Planarity : 0.006 0.063 758 Dihedral : 6.484 28.111 579 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.43 % Allowed : 4.96 % Favored : 94.61 % 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: -1.11 (0.36), residues: 515 helix: -0.08 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -2.52 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 314 HIS 0.004 0.001 HIS B 447 PHE 0.027 0.003 PHE B 578 TYR 0.024 0.002 TYR B 317 ARG 0.010 0.001 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.9369 (mm) cc_final: 0.9099 (mm) REVERT: B 210 ASN cc_start: 0.9255 (m110) cc_final: 0.8929 (t0) REVERT: B 329 MET cc_start: 0.9049 (pmm) cc_final: 0.8668 (pmm) REVERT: B 486 ASP cc_start: 0.8852 (m-30) cc_final: 0.8581 (m-30) REVERT: B 548 PHE cc_start: 0.8762 (m-80) cc_final: 0.8457 (m-80) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.2286 time to fit residues: 15.6054 Evaluate side-chains 41 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** B 508 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 = 0.3454 r_free = 0.3454 target = 0.061065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050003 restraints weight = 46263.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.051207 restraints weight = 30927.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052086 restraints weight = 23203.384| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4419 Z= 0.213 Angle : 0.757 12.595 5951 Z= 0.401 Chirality : 0.046 0.333 652 Planarity : 0.005 0.052 758 Dihedral : 6.245 26.949 579 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.43 % Allowed : 3.02 % Favored : 96.55 % 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 (0.36), residues: 515 helix: 0.25 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -2.58 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.009 0.001 HIS B 447 PHE 0.020 0.003 PHE B 409 TYR 0.015 0.002 TYR B 482 ARG 0.006 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.9452 (mm) cc_final: 0.9175 (mm) REVERT: B 204 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: B 210 ASN cc_start: 0.9298 (m110) cc_final: 0.8985 (t0) REVERT: B 267 MET cc_start: 0.5923 (mmt) cc_final: 0.5225 (mmt) REVERT: B 329 MET cc_start: 0.9193 (pmm) cc_final: 0.8824 (pmm) REVERT: B 419 HIS cc_start: 0.8829 (m-70) cc_final: 0.8349 (m90) REVERT: B 486 ASP cc_start: 0.8847 (m-30) cc_final: 0.8630 (m-30) REVERT: B 548 PHE cc_start: 0.8783 (m-10) cc_final: 0.8492 (m-80) REVERT: B 549 ARG cc_start: 0.9009 (ptm-80) cc_final: 0.8704 (ptt180) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.2291 time to fit residues: 15.5702 Evaluate side-chains 41 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049156 restraints weight = 44690.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050235 restraints weight = 32650.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051000 restraints weight = 25729.189| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4419 Z= 0.193 Angle : 0.725 10.931 5951 Z= 0.374 Chirality : 0.044 0.305 652 Planarity : 0.005 0.053 758 Dihedral : 6.022 27.769 579 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.22 % Allowed : 3.88 % Favored : 95.91 % 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: -0.58 (0.36), residues: 515 helix: 0.41 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.80 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.006 0.001 HIS B 271 PHE 0.039 0.002 PHE B 13 TYR 0.022 0.002 TYR B 402 ARG 0.006 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.9399 (mm) cc_final: 0.9033 (mm) REVERT: B 210 ASN cc_start: 0.9186 (m110) cc_final: 0.8766 (t0) REVERT: B 329 MET cc_start: 0.9169 (pmm) cc_final: 0.8783 (pmm) REVERT: B 419 HIS cc_start: 0.8726 (m-70) cc_final: 0.8266 (m90) REVERT: B 440 MET cc_start: 0.8813 (mmp) cc_final: 0.8603 (tpp) REVERT: B 486 ASP cc_start: 0.8830 (m-30) cc_final: 0.8576 (m-30) REVERT: B 548 PHE cc_start: 0.8788 (m-10) cc_final: 0.8503 (m-80) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2001 time to fit residues: 13.8853 Evaluate side-chains 39 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 chunk 12 optimal weight: 4.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.069012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059249 restraints weight = 46328.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060392 restraints weight = 29170.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.061015 restraints weight = 20609.175| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4419 Z= 0.186 Angle : 0.696 10.842 5951 Z= 0.362 Chirality : 0.045 0.301 652 Planarity : 0.005 0.064 758 Dihedral : 5.823 27.165 579 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.20 % 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: -0.36 (0.36), residues: 515 helix: 0.63 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -2.81 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.004 0.001 HIS B 447 PHE 0.030 0.002 PHE B 396 TYR 0.019 0.002 TYR B 402 ARG 0.004 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9169 (m110) cc_final: 0.8819 (t0) REVERT: B 419 HIS cc_start: 0.8703 (m-70) cc_final: 0.8219 (m90) REVERT: B 440 MET cc_start: 0.8946 (mmp) cc_final: 0.8581 (tpt) REVERT: B 441 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8743 (mp0) REVERT: B 484 MET cc_start: 0.9512 (mmp) cc_final: 0.9260 (ptt) REVERT: B 486 ASP cc_start: 0.8841 (m-30) cc_final: 0.8586 (m-30) REVERT: B 548 PHE cc_start: 0.8766 (m-10) cc_final: 0.8472 (m-80) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.2007 time to fit residues: 14.4263 Evaluate side-chains 38 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 HIS ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.069143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059358 restraints weight = 45505.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.060472 restraints weight = 28491.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061227 restraints weight = 20288.270| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4419 Z= 0.186 Angle : 0.709 12.405 5951 Z= 0.367 Chirality : 0.045 0.386 652 Planarity : 0.006 0.104 758 Dihedral : 5.798 28.869 579 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -0.33 (0.37), residues: 515 helix: 0.66 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -2.81 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.009 0.001 HIS B 479 PHE 0.015 0.002 PHE B 13 TYR 0.018 0.002 TYR B 482 ARG 0.008 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9154 (m110) cc_final: 0.8831 (t0) REVERT: B 319 LEU cc_start: 0.9480 (tp) cc_final: 0.8957 (tp) REVERT: B 419 HIS cc_start: 0.8706 (m-70) cc_final: 0.8229 (m90) REVERT: B 440 MET cc_start: 0.8917 (mmp) cc_final: 0.8630 (tpt) REVERT: B 453 MET cc_start: 0.8260 (ppp) cc_final: 0.7785 (ppp) REVERT: B 484 MET cc_start: 0.9512 (mmp) cc_final: 0.9280 (ptt) REVERT: B 486 ASP cc_start: 0.8834 (m-30) cc_final: 0.8576 (m-30) REVERT: B 548 PHE cc_start: 0.8769 (m-10) cc_final: 0.8467 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2055 time to fit residues: 12.9440 Evaluate side-chains 39 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.070060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.060242 restraints weight = 45248.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.061297 restraints weight = 27925.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.062020 restraints weight = 19972.511| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4419 Z= 0.175 Angle : 0.698 11.306 5951 Z= 0.359 Chirality : 0.044 0.315 652 Planarity : 0.006 0.081 758 Dihedral : 5.644 28.670 579 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -0.28 (0.37), residues: 515 helix: 0.65 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.80 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 314 HIS 0.006 0.001 HIS B 479 PHE 0.026 0.002 PHE B 409 TYR 0.018 0.001 TYR B 482 ARG 0.004 0.000 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9121 (m110) cc_final: 0.8835 (t0) REVERT: B 419 HIS cc_start: 0.8774 (m-70) cc_final: 0.8286 (m90) REVERT: B 450 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7852 (mtp180) REVERT: B 453 MET cc_start: 0.8298 (ppp) cc_final: 0.7884 (ppp) REVERT: B 484 MET cc_start: 0.9495 (mmp) cc_final: 0.9286 (ptt) REVERT: B 486 ASP cc_start: 0.8837 (m-30) cc_final: 0.8575 (m-30) REVERT: B 548 PHE cc_start: 0.8784 (m-10) cc_final: 0.8515 (m-80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1949 time to fit residues: 12.5297 Evaluate side-chains 42 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.070431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.060450 restraints weight = 44408.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.061621 restraints weight = 28342.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.062405 restraints weight = 20147.167| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4419 Z= 0.170 Angle : 0.672 10.721 5951 Z= 0.347 Chirality : 0.043 0.288 652 Planarity : 0.005 0.067 758 Dihedral : 5.510 28.379 579 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -0.20 (0.36), residues: 515 helix: 0.69 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -2.73 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.004 0.001 HIS B 479 PHE 0.013 0.001 PHE B 203 TYR 0.018 0.001 TYR B 482 ARG 0.007 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9127 (m110) cc_final: 0.8854 (t0) REVERT: B 419 HIS cc_start: 0.8758 (m-70) cc_final: 0.8297 (m90) REVERT: B 441 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8886 (mp0) REVERT: B 450 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7751 (mtp180) REVERT: B 453 MET cc_start: 0.8379 (ppp) cc_final: 0.8004 (ppp) REVERT: B 484 MET cc_start: 0.9495 (mmp) cc_final: 0.9285 (ptt) REVERT: B 486 ASP cc_start: 0.8839 (m-30) cc_final: 0.8583 (m-30) REVERT: B 548 PHE cc_start: 0.8792 (m-10) cc_final: 0.8547 (m-80) REVERT: B 549 ARG cc_start: 0.8940 (ptm-80) cc_final: 0.8607 (ptt90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2034 time to fit residues: 12.9731 Evaluate side-chains 42 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.068949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059008 restraints weight = 46331.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.060151 restraints weight = 29593.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.060949 restraints weight = 21156.095| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4419 Z= 0.198 Angle : 0.706 12.661 5951 Z= 0.369 Chirality : 0.045 0.431 652 Planarity : 0.006 0.069 758 Dihedral : 5.504 28.987 579 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.14 (0.37), residues: 515 helix: 0.75 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.003 0.001 HIS B 426 PHE 0.021 0.002 PHE B 409 TYR 0.018 0.002 TYR B 482 ARG 0.008 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9157 (m110) cc_final: 0.8918 (t0) REVERT: B 419 HIS cc_start: 0.8795 (m-70) cc_final: 0.8314 (m90) REVERT: B 422 VAL cc_start: 0.9218 (t) cc_final: 0.8975 (t) REVERT: B 426 HIS cc_start: 0.9502 (m90) cc_final: 0.9202 (m90) REVERT: B 450 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7888 (mtp180) REVERT: B 453 MET cc_start: 0.8344 (ppp) cc_final: 0.7965 (ppp) REVERT: B 484 MET cc_start: 0.9491 (mmp) cc_final: 0.9275 (ptt) REVERT: B 486 ASP cc_start: 0.8860 (m-30) cc_final: 0.8610 (m-30) REVERT: B 548 PHE cc_start: 0.8815 (m-10) cc_final: 0.8548 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2171 time to fit residues: 13.5213 Evaluate side-chains 39 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 4 optimal weight: 0.0370 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS ** B 364 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.070681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060634 restraints weight = 44150.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.061781 restraints weight = 28218.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062590 restraints weight = 20118.715| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4419 Z= 0.175 Angle : 0.692 12.067 5951 Z= 0.358 Chirality : 0.045 0.405 652 Planarity : 0.005 0.070 758 Dihedral : 5.443 29.505 579 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.07 (0.37), residues: 515 helix: 0.80 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 314 HIS 0.004 0.001 HIS B 479 PHE 0.037 0.002 PHE B 475 TYR 0.018 0.001 TYR B 482 ARG 0.007 0.001 ARG B 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LEU cc_start: 0.9472 (mm) cc_final: 0.9123 (pp) REVERT: B 419 HIS cc_start: 0.8838 (m-70) cc_final: 0.8380 (m90) REVERT: B 422 VAL cc_start: 0.9209 (t) cc_final: 0.8959 (t) REVERT: B 426 HIS cc_start: 0.9497 (m90) cc_final: 0.9190 (m90) REVERT: B 450 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7650 (mtp180) REVERT: B 453 MET cc_start: 0.8404 (ppp) cc_final: 0.8052 (ppp) REVERT: B 484 MET cc_start: 0.9471 (mmp) cc_final: 0.9249 (ptt) REVERT: B 486 ASP cc_start: 0.8853 (m-30) cc_final: 0.8591 (m-30) REVERT: B 548 PHE cc_start: 0.8787 (m-10) cc_final: 0.8510 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2151 time to fit residues: 14.3747 Evaluate side-chains 43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.067777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058005 restraints weight = 46373.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.059146 restraints weight = 30001.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.059939 restraints weight = 21648.298| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4419 Z= 0.219 Angle : 0.742 12.637 5951 Z= 0.394 Chirality : 0.046 0.403 652 Planarity : 0.005 0.070 758 Dihedral : 5.530 30.236 579 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -0.08 (0.37), residues: 515 helix: 0.80 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -2.66 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.005 0.001 HIS B 209 PHE 0.030 0.002 PHE B 475 TYR 0.021 0.002 TYR B 207 ARG 0.009 0.001 ARG B 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1608.51 seconds wall clock time: 29 minutes 43.74 seconds (1783.74 seconds total)