Starting phenix.real_space_refine (version: dev) on Sun Oct 3 09:06:41 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/10_2021/7ryq_24745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/10_2021/7ryq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/10_2021/7ryq_24745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/10_2021/7ryq_24745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/10_2021/7ryq_24745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/10_2021/7ryq_24745.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ASP 107": "OD1" <-> "OD2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4376/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: 2.77, per 1000 atoms: 0.64 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 703.5 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: 0.17 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: 1.13 Time building geometry restraints manager: 2.10 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: 97.74 - 105.00: 51 105.00 - 112.27: 2220 112.27 - 119.53: 1488 119.53 - 126.79: 2147 126.79 - 134.05: 45 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 2.520 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. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.720 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.030 Process input model: 16.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.200 Set ADP refinement strategy: 0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 37.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.68 % Favored : 88.93 % Rotamer Outliers : 6.25 % 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 *********************** 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 fitting. rotamer outliers: 29 poor density : 57 time to evaluate : 0.540 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 outliers start: 29 outliers final: 12 residues processed: 82 average time/residue: 0.2263 time to fit residues: 22.1802 Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1720 time to fit residues: 3.2749 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0400 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2412 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= 0.210 Angle : 0.744 12.879 5951 Z= 0.391 Chirality : 0.045 0.301 652 Planarity : 0.005 0.066 758 Dihedral : 6.280 27.267 579 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.65 % 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: -0.91 (0.36), residues: 515 helix: 0.09 (0.25), residues: 387 sheet: None (None), residues: 0 loop : -2.56 (0.53), residues: 128 *********************** 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 55 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 55 average time/residue: 0.1980 time to fit residues: 13.7104 Evaluate side-chains 36 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7668 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3212 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= 0.193 Angle : 0.698 10.921 5951 Z= 0.367 Chirality : 0.043 0.270 652 Planarity : 0.005 0.052 758 Dihedral : 5.968 26.991 579 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.22 % 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: -0.60 (0.36), residues: 515 helix: 0.36 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.65 (0.52), residues: 128 *********************** 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 fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.2139 time to fit residues: 15.5788 Evaluate side-chains 37 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7305 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4419 Z= 0.262 Angle : 0.775 12.379 5951 Z= 0.413 Chirality : 0.046 0.340 652 Planarity : 0.005 0.063 758 Dihedral : 6.322 27.502 579 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.22 % 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: -0.95 (0.36), residues: 515 helix: 0.10 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -2.62 (0.52), residues: 134 *********************** 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 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2146 time to fit residues: 14.1185 Evaluate side-chains 38 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7498 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0570 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN B 426 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4129 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= 0.171 Angle : 0.664 11.957 5951 Z= 0.346 Chirality : 0.043 0.346 652 Planarity : 0.005 0.053 758 Dihedral : 5.763 27.875 579 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 0.00 % 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: -0.64 (0.36), residues: 515 helix: 0.36 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.80 (0.51), residues: 127 *********************** 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 52 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1971 time to fit residues: 12.8700 Evaluate side-chains 38 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7268 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.0020 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 B 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 4419 Z= 0.179 Angle : 0.662 12.079 5951 Z= 0.342 Chirality : 0.043 0.360 652 Planarity : 0.006 0.114 758 Dihedral : 5.590 28.769 579 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % 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: -0.31 (0.37), residues: 515 helix: 0.62 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.77 (0.52), residues: 126 *********************** 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 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1945 time to fit residues: 12.0488 Evaluate side-chains 37 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7470 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.0010 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 20 optimal weight: 0.0050 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN B 364 GLN B 508 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 4419 Z= 0.162 Angle : 0.667 10.969 5951 Z= 0.335 Chirality : 0.043 0.295 652 Planarity : 0.005 0.063 758 Dihedral : 5.353 28.163 579 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.00 % 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 (0.37), residues: 515 helix: 0.70 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 126 *********************** 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 fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1982 time to fit residues: 12.8113 Evaluate side-chains 42 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7584 ------------------------------------------------------------------------------- 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: 0.0060 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS B 323 GLN B 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 4419 Z= 0.168 Angle : 0.664 11.670 5951 Z= 0.340 Chirality : 0.043 0.383 652 Planarity : 0.005 0.064 758 Dihedral : 5.231 29.486 579 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.37), residues: 515 helix: 0.83 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 126 *********************** 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2072 time to fit residues: 13.0522 Evaluate side-chains 42 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7446 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN B 510 ASN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 4419 Z= 0.175 Angle : 0.676 11.762 5951 Z= 0.346 Chirality : 0.044 0.372 652 Planarity : 0.005 0.066 758 Dihedral : 5.187 29.223 579 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: 0.08 (0.37), residues: 515 helix: 0.89 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -2.72 (0.54), residues: 121 *********************** 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2002 time to fit residues: 12.7965 Evaluate side-chains 39 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7265 ------------------------------------------------------------------------------- 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: 0.0060 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 4419 Z= 0.183 Angle : 0.694 11.668 5951 Z= 0.359 Chirality : 0.044 0.359 652 Planarity : 0.005 0.066 758 Dihedral : 5.225 29.297 579 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.37), residues: 515 helix: 0.82 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -2.63 (0.55), residues: 121 ********************** 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 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1886 time to fit residues: 11.5963 Evaluate side-chains 43 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7410 ------------------------------------------------------------------------------- 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: 0.0870 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.0010 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN ** B 518 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 = 0.3538 r_free = 0.3538 target = 0.068599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058272 restraints weight = 44313.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.059420 restraints weight = 28840.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.060206 restraints weight = 20926.710| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. BOND : 0.003 0.049 4419 Z= 0.176 ANGLE : 0.696 11.498 5951 Z= 0.354 CHIRALITY : 0.044 0.349 652 PLANARITY : 0.005 0.066 758 DIHEDRAL : 5.074 28.833 579 MIN NONBONDED DISTANCE : 2.147 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 15.12 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.63 % FAVORED : 94.37 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 0.11 (0.37), RESIDUES: 515 HELIX: 0.86 (0.26), RESIDUES: 398 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -2.62 (0.56), RESIDUES: 117 ------------------------------------------------------------------------------- Occupancy refinement ******************** GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES. BOND : 0.003 0.049 4419 Z= 0.176 ANGLE : 0.696 11.498 5951 Z= 0.354 CHIRALITY : 0.044 0.349 652 PLANARITY : 0.005 0.066 758 DIHEDRAL : 5.074 28.833 579 MIN NONBONDED DISTANCE : 2.147 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 15.12 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.63 % FAVORED : 94.37 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 0.11 (0.37), RESIDUES: 515 HELIX: 0.86 (0.26), RESIDUES: 398 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -2.62 (0.56), RESIDUES: 117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 4419 Z= 0.176 Angle : 0.696 11.498 5951 Z= 0.354 Chirality : 0.044 0.349 652 Planarity : 0.005 0.066 758 Dihedral : 5.074 28.833 579 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.37), residues: 515 helix: 0.86 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -2.62 (0.56), residues: 117 =============================================================================== Job complete usr+sys time: 1217.57 seconds wall clock time: 23 minutes 5.46 seconds (1385.46 seconds total)