Starting phenix.real_space_refine (version: dev) on Fri Feb 17 09:34:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/02_2023/7ryq_24745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/02_2023/7ryq_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_24745/02_2023/7ryq_24745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/02_2023/7ryq_24745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/02_2023/7ryq_24745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryq_24745/02_2023/7ryq_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 Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 2.95, per 1000 atoms: 0.68 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 494.1 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: 0.18 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: 1.14 Time building geometry restraints manager: 1.91 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. 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 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 Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 6.050 Check model and map are aligned: 0.060 Process input model: 15.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.230 ------------------------------------------------------------------------------- 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 : 39.25 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 : 0.497 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: 0.2420 time to fit residues: 23.5423 Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1397 time to fit residues: 2.7905 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9980 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2066 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= 0.221 Angle : 0.790 13.525 5951 Z= 0.411 Chirality : 0.045 0.299 652 Planarity : 0.005 0.063 758 Dihedral : 6.477 27.163 579 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.36), residues: 515 helix: -0.15 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -2.58 (0.53), residues: 129 *********************** 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 58 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 58 average time/residue: 0.2413 time to fit residues: 16.8745 Evaluate side-chains 37 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7008 ------------------------------------------------------------------------------- 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: 0.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 474 GLN ** 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: 0.7491 moved from start: 0.2710 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= 0.191 Angle : 0.728 12.052 5951 Z= 0.378 Chirality : 0.044 0.297 652 Planarity : 0.005 0.050 758 Dihedral : 6.128 27.488 579 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % 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: -0.83 (0.36), residues: 515 helix: 0.16 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -2.66 (0.52), residues: 123 *********************** 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 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.499 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: 54 average time/residue: 0.2009 time to fit residues: 13.4779 Evaluate side-chains 36 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6520 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 B 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3016 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= 0.218 Angle : 0.715 11.637 5951 Z= 0.379 Chirality : 0.043 0.305 652 Planarity : 0.005 0.053 758 Dihedral : 6.112 28.431 579 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.82 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: -0.71 (0.36), residues: 515 helix: 0.31 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.79 (0.51), residues: 128 *********************** 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 55 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.2121 time to fit residues: 14.4828 Evaluate side-chains 37 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8045 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4419 Z= 0.221 Angle : 0.719 12.126 5951 Z= 0.381 Chirality : 0.045 0.357 652 Planarity : 0.005 0.051 758 Dihedral : 6.103 28.733 579 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % 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: -0.77 (0.36), residues: 515 helix: 0.26 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.83 (0.51), residues: 126 *********************** 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 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.557 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: 56 average time/residue: 0.2270 time to fit residues: 15.6629 Evaluate side-chains 38 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6980 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS B 364 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4419 Z= 0.187 Angle : 0.700 12.170 5951 Z= 0.364 Chirality : 0.044 0.380 652 Planarity : 0.006 0.110 758 Dihedral : 5.963 29.401 579 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -0.60 (0.36), residues: 515 helix: 0.44 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.94 (0.50), residues: 127 *********************** 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 55 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2344 time to fit residues: 15.8909 Evaluate side-chains 39 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8733 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 4419 Z= 0.190 Angle : 0.713 11.392 5951 Z= 0.371 Chirality : 0.044 0.302 652 Planarity : 0.005 0.066 758 Dihedral : 5.864 29.859 579 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -0.53 (0.36), residues: 515 helix: 0.48 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.89 (0.50), residues: 128 *********************** 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 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.556 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: 50 average time/residue: 0.1991 time to fit residues: 12.6690 Evaluate side-chains 39 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6945 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.0270 chunk 43 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4327 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 : 0.705 12.098 5951 Z= 0.367 Chirality : 0.045 0.419 652 Planarity : 0.006 0.105 758 Dihedral : 5.735 28.817 579 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -0.49 (0.36), residues: 515 helix: 0.52 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.89 (0.51), residues: 128 *********************** 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 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1891 time to fit residues: 12.6900 Evaluate side-chains 40 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7116 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.0030 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN B 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 4419 Z= 0.174 Angle : 0.707 11.984 5951 Z= 0.362 Chirality : 0.045 0.377 652 Planarity : 0.005 0.065 758 Dihedral : 5.655 30.011 579 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 0.00 % 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: -0.59 (0.36), residues: 515 helix: 0.43 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.85 (0.50), residues: 128 *********************** 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 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1882 time to fit residues: 12.2929 Evaluate side-chains 41 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7174 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 0.0270 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4854 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= 0.188 Angle : 0.706 11.934 5951 Z= 0.363 Chirality : 0.045 0.372 652 Planarity : 0.005 0.070 758 Dihedral : 5.580 29.281 579 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.78 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: -0.32 (0.36), residues: 515 helix: 0.61 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.74 (0.50), residues: 127 ********************** 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.537 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: 50 average time/residue: 0.2208 time to fit residues: 13.7527 Evaluate side-chains 41 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7320 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3561 r_free = 0.3561 target = 0.068537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.058558 restraints weight = 45380.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059652 restraints weight = 29057.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.060445 restraints weight = 20928.855| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 4419 Z= 0.209 Angle : 0.698 12.001 5951 Z= 0.366 Chirality : 0.044 0.359 652 Planarity : 0.005 0.066 758 Dihedral : 5.565 29.891 579 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % 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: -0.36 (0.36), residues: 515 helix: 0.57 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.71 (0.52), residues: 127 =============================================================================== Job complete usr+sys time: 1243.61 seconds wall clock time: 23 minutes 16.49 seconds (1396.49 seconds total)