Starting phenix.real_space_refine on Fri Dec 27 11:24:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryq_24745/12_2024/7ryq_24745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryq_24745/12_2024/7ryq_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_24745/12_2024/7ryq_24745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryq_24745/12_2024/7ryq_24745.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryq_24745/12_2024/7ryq_24745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryq_24745/12_2024/7ryq_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.35, per 1000 atoms: 0.77 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: 1.24 Conformation dependent library (CDL) restraints added in 490.7 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: 0.40 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: 1.22 Time building geometry restraints manager: 1.38 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: 1.630 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.520 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- 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 : 0.508 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: 0.2375 time to fit residues: 23.2620 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 : 0.532 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.9354 (mm) cc_final: 0.9104 (mm) REVERT: B 210 ASN cc_start: 0.9238 (m110) cc_final: 0.8839 (t0) REVERT: B 329 MET cc_start: 0.9062 (pmm) cc_final: 0.8703 (pmm) REVERT: B 486 ASP cc_start: 0.8836 (m-30) cc_final: 0.8557 (m-30) REVERT: B 548 PHE cc_start: 0.8679 (m-80) cc_final: 0.8368 (m-80) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.2426 time to fit residues: 16.5438 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 : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2777 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= 0.203 Angle : 0.749 12.354 5951 Z= 0.391 Chirality : 0.046 0.340 652 Planarity : 0.005 0.052 758 Dihedral : 6.130 26.275 579 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.43 % Allowed : 3.23 % Favored : 96.34 % 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: -0.69 (0.36), residues: 515 helix: 0.28 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.61 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.011 0.001 HIS B 447 PHE 0.026 0.002 PHE B 409 TYR 0.015 0.002 TYR B 516 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 59 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.9333 (mm) cc_final: 0.9064 (mm) REVERT: B 204 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6280 (pm20) REVERT: B 210 ASN cc_start: 0.9214 (m110) cc_final: 0.8886 (t0) REVERT: B 329 MET cc_start: 0.9089 (pmm) cc_final: 0.8741 (pmm) REVERT: B 419 HIS cc_start: 0.8520 (m-70) cc_final: 0.8057 (m90) REVERT: B 486 ASP cc_start: 0.8776 (m-30) cc_final: 0.8524 (m-30) REVERT: B 548 PHE cc_start: 0.8673 (m-10) cc_final: 0.8371 (m-80) REVERT: B 549 ARG cc_start: 0.8971 (ptm-80) cc_final: 0.8695 (ptt180) outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.2246 time to fit residues: 16.1521 Evaluate side-chains 43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4419 Z= 0.194 Angle : 0.721 10.921 5951 Z= 0.375 Chirality : 0.044 0.305 652 Planarity : 0.005 0.053 758 Dihedral : 5.987 28.414 579 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.22 % Allowed : 3.45 % Favored : 96.34 % 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: -0.54 (0.36), residues: 515 helix: 0.45 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.84 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.005 0.001 HIS B 447 PHE 0.039 0.003 PHE B 13 TYR 0.017 0.002 TYR B 317 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 : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LEU cc_start: 0.9347 (mm) cc_final: 0.9061 (mm) REVERT: B 210 ASN cc_start: 0.9198 (m110) cc_final: 0.8786 (t0) REVERT: B 329 MET cc_start: 0.9113 (pmm) cc_final: 0.8740 (pmm) REVERT: B 419 HIS cc_start: 0.8531 (m-70) cc_final: 0.8078 (m90) REVERT: B 486 ASP cc_start: 0.8794 (m-30) cc_final: 0.8522 (m-30) REVERT: B 548 PHE cc_start: 0.8692 (m-10) cc_final: 0.8376 (m-80) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2012 time to fit residues: 14.0708 Evaluate side-chains 40 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 overall best weight: 0.8238 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3541 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= 0.185 Angle : 0.687 10.728 5951 Z= 0.359 Chirality : 0.044 0.305 652 Planarity : 0.005 0.065 758 Dihedral : 5.792 27.636 579 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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: -0.33 (0.36), residues: 515 helix: 0.65 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -2.80 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS B 245 PHE 0.024 0.002 PHE B 409 TYR 0.016 0.001 TYR B 482 ARG 0.004 0.000 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9145 (m110) cc_final: 0.8763 (t0) REVERT: B 329 MET cc_start: 0.9120 (pmm) cc_final: 0.8716 (pmm) REVERT: B 419 HIS cc_start: 0.8627 (m-70) cc_final: 0.8155 (m90) REVERT: B 484 MET cc_start: 0.9550 (mmp) cc_final: 0.9303 (ptt) REVERT: B 486 ASP cc_start: 0.8837 (m-30) cc_final: 0.8560 (m-30) REVERT: B 548 PHE cc_start: 0.8677 (m-10) cc_final: 0.8370 (m-80) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2044 time to fit residues: 14.4491 Evaluate side-chains 40 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 48 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4024 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= 0.181 Angle : 0.698 12.390 5951 Z= 0.364 Chirality : 0.045 0.385 652 Planarity : 0.005 0.057 758 Dihedral : 5.648 28.176 579 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.36), residues: 515 helix: 0.55 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.84 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 314 HIS 0.009 0.001 HIS B 479 PHE 0.018 0.002 PHE B 396 TYR 0.015 0.001 TYR B 402 ARG 0.006 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 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9097 (m110) cc_final: 0.8747 (t0) REVERT: B 419 HIS cc_start: 0.8666 (m-70) cc_final: 0.8208 (m90) REVERT: B 453 MET cc_start: 0.8040 (ppp) cc_final: 0.7565 (ppp) REVERT: B 486 ASP cc_start: 0.8905 (m-30) cc_final: 0.8598 (m-30) REVERT: B 548 PHE cc_start: 0.8674 (m-10) cc_final: 0.8373 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2240 time to fit residues: 14.4175 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 : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4289 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= 0.180 Angle : 0.680 11.453 5951 Z= 0.349 Chirality : 0.044 0.314 652 Planarity : 0.005 0.065 758 Dihedral : 5.489 28.563 579 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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: -0.36 (0.36), residues: 515 helix: 0.58 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.76 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 314 HIS 0.005 0.001 HIS B 479 PHE 0.023 0.002 PHE B 409 TYR 0.010 0.001 TYR B 207 ARG 0.004 0.001 ARG B 450 *********************** 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 : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9123 (m110) cc_final: 0.8821 (t0) REVERT: B 419 HIS cc_start: 0.8617 (m-70) cc_final: 0.8157 (m90) REVERT: B 450 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7723 (mtp180) REVERT: B 453 MET cc_start: 0.8286 (ppp) cc_final: 0.7867 (ppp) REVERT: B 486 ASP cc_start: 0.8950 (m-30) cc_final: 0.8672 (m-30) REVERT: B 548 PHE cc_start: 0.8703 (m-10) cc_final: 0.8459 (m-80) REVERT: B 549 ARG cc_start: 0.8967 (ptm-80) cc_final: 0.8672 (ptt90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2157 time to fit residues: 13.6451 Evaluate side-chains 40 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 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 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4357 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= 0.186 Angle : 0.694 10.826 5951 Z= 0.359 Chirality : 0.043 0.290 652 Planarity : 0.005 0.068 758 Dihedral : 5.490 28.947 579 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.37), residues: 515 helix: 0.72 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.71 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.008 0.001 HIS B 447 PHE 0.013 0.002 PHE B 203 TYR 0.038 0.002 TYR B 482 ARG 0.004 0.000 ARG B 450 *********************** 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 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9140 (m110) cc_final: 0.8856 (t0) REVERT: B 419 HIS cc_start: 0.8539 (m-70) cc_final: 0.8103 (m90) REVERT: B 450 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7408 (mtp180) REVERT: B 453 MET cc_start: 0.8290 (ppp) cc_final: 0.7868 (ppp) REVERT: B 486 ASP cc_start: 0.8913 (m-30) cc_final: 0.8613 (m-30) REVERT: B 548 PHE cc_start: 0.8699 (m-10) cc_final: 0.8441 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2237 time to fit residues: 14.0529 Evaluate side-chains 40 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4534 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= 0.179 Angle : 0.710 12.491 5951 Z= 0.366 Chirality : 0.046 0.426 652 Planarity : 0.005 0.069 758 Dihedral : 5.482 28.757 579 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 (0.37), residues: 515 helix: 0.76 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.77 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.006 0.001 HIS B 447 PHE 0.034 0.002 PHE B 475 TYR 0.027 0.001 TYR B 482 ARG 0.004 0.000 ARG B 450 *********************** 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 : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9127 (m110) cc_final: 0.8867 (t0) REVERT: B 419 HIS cc_start: 0.8535 (m-70) cc_final: 0.8090 (m90) REVERT: B 450 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7488 (mtp180) REVERT: B 453 MET cc_start: 0.8271 (ppp) cc_final: 0.7884 (ppp) REVERT: B 484 MET cc_start: 0.9488 (mmp) cc_final: 0.9246 (ptt) REVERT: B 486 ASP cc_start: 0.8910 (m-30) cc_final: 0.8603 (m-30) REVERT: B 548 PHE cc_start: 0.8694 (m-10) cc_final: 0.8440 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2209 time to fit residues: 13.8156 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4419 Z= 0.174 Angle : 0.707 12.218 5951 Z= 0.364 Chirality : 0.045 0.406 652 Planarity : 0.005 0.070 758 Dihedral : 5.415 30.071 579 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.07 (0.37), residues: 515 helix: 0.79 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -2.70 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 314 HIS 0.007 0.001 HIS B 447 PHE 0.032 0.002 PHE B 475 TYR 0.028 0.002 TYR B 402 ARG 0.003 0.000 ARG B 359 ********************** 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 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.9061 (m110) cc_final: 0.8856 (t0) REVERT: B 419 HIS cc_start: 0.8521 (m-70) cc_final: 0.8088 (m90) REVERT: B 453 MET cc_start: 0.8272 (ppp) cc_final: 0.7895 (ppp) REVERT: B 484 MET cc_start: 0.9500 (mmp) cc_final: 0.9271 (ptt) REVERT: B 486 ASP cc_start: 0.8897 (m-30) cc_final: 0.8596 (m-30) REVERT: B 548 PHE cc_start: 0.8710 (m-10) cc_final: 0.8475 (m-80) REVERT: B 549 ARG cc_start: 0.8979 (ptm-80) cc_final: 0.8742 (ptt180) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2262 time to fit residues: 13.8650 Evaluate side-chains 44 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- 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 479 HIS ** 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 = 0.3580 r_free = 0.3580 target = 0.069467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.059515 restraints weight = 44993.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060627 restraints weight = 29073.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.061402 restraints weight = 20669.805| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4419 Z= 0.178 Angle : 0.730 12.227 5951 Z= 0.378 Chirality : 0.045 0.397 652 Planarity : 0.005 0.070 758 Dihedral : 5.384 29.856 579 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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 : 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 (0.36), residues: 515 helix: 0.89 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -2.66 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.007 0.001 HIS B 447 PHE 0.034 0.002 PHE B 475 TYR 0.026 0.002 TYR B 402 ARG 0.004 0.000 ARG B 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.31 seconds wall clock time: 24 minutes 9.76 seconds (1449.76 seconds total)