Starting phenix.real_space_refine on Mon Mar 11 01:13:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo9_33341/03_2024/7xo9_33341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo9_33341/03_2024/7xo9_33341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo9_33341/03_2024/7xo9_33341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo9_33341/03_2024/7xo9_33341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo9_33341/03_2024/7xo9_33341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo9_33341/03_2024/7xo9_33341.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4154 2.51 5 N 1074 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 589": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6483 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1582 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4901 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'peptide': 595, 'undetermined': 5} Link IDs: {'PTRANS': 27, 'TRANS': 567, None: 5} Not linked: pdbres="TYR D 613 " pdbres=" CL D 901 " Not linked: pdbres=" CL D 901 " pdbres=" ZN D 902 " Not linked: pdbres=" ZN D 902 " pdbres="NAG D 903 " Not linked: pdbres="NAG D 903 " pdbres="NAG D 904 " Not linked: pdbres="NAG D 904 " pdbres="NAG D 905 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.98, per 1000 atoms: 0.61 Number of scatterers: 6483 At special positions: 0 Unit cell: (97.232, 70.864, 117.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1216 8.00 N 1074 7.00 C 4154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 Links applied NAG-ASN " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 90 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 55.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.606A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.776A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.653A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.617A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.002A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.616A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.649A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.956A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.750A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.867A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.671A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 531 removed outlier: 3.542A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.743A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.597A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.540A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.645A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.073A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.027A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 846 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: 1.77 Time building geometry restraints manager: 2.79 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: 2040 1.34 - 1.45: 1106 1.45 - 1.57: 3462 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6666 Sorted by residual: bond pdb=" N ASN D 322 " pdb=" CA ASN D 322 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.31e-02 5.83e+03 4.65e+00 bond pdb=" N SER D 19 " pdb=" CA SER D 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" C3 NAG D 904 " pdb=" O3 NAG D 904 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C3 NAG D 905 " pdb=" O3 NAG D 905 " ideal model delta sigma weight residual 1.403 1.429 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 6661 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.10: 226 107.10 - 113.82: 3531 113.82 - 120.55: 2772 120.55 - 127.27: 2430 127.27 - 134.00: 101 Bond angle restraints: 9060 Sorted by residual: angle pdb=" C ASN D 322 " pdb=" CA ASN D 322 " pdb=" CB ASN D 322 " ideal model delta sigma weight residual 109.76 116.39 -6.63 1.99e+00 2.53e-01 1.11e+01 angle pdb=" C ASN D 322 " pdb=" N MET D 323 " pdb=" CA MET D 323 " ideal model delta sigma weight residual 120.87 126.40 -5.53 1.69e+00 3.50e-01 1.07e+01 angle pdb=" CA ASN D 322 " pdb=" C ASN D 322 " pdb=" O ASN D 322 " ideal model delta sigma weight residual 121.81 118.90 2.91 1.18e+00 7.18e-01 6.09e+00 angle pdb=" N ILE D 544 " pdb=" CA ILE D 544 " pdb=" C ILE D 544 " ideal model delta sigma weight residual 112.98 110.04 2.94 1.25e+00 6.40e-01 5.53e+00 angle pdb=" O PRO D 321 " pdb=" C PRO D 321 " pdb=" N ASN D 322 " ideal model delta sigma weight residual 123.06 120.18 2.88 1.23e+00 6.61e-01 5.48e+00 ... (remaining 9055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3643 17.84 - 35.69: 249 35.69 - 53.53: 43 53.53 - 71.37: 13 71.37 - 89.22: 6 Dihedral angle restraints: 3954 sinusoidal: 1626 harmonic: 2328 Sorted by residual: dihedral pdb=" CA LYS D 68 " pdb=" CB LYS D 68 " pdb=" CG LYS D 68 " pdb=" CD LYS D 68 " ideal model delta sinusoidal sigma weight residual 180.00 120.09 59.91 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS D 341 " pdb=" CA LYS D 341 " pdb=" CB LYS D 341 " pdb=" CG LYS D 341 " ideal model delta sinusoidal sigma weight residual -180.00 -121.74 -58.26 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET D 323 " pdb=" CG MET D 323 " pdb=" SD MET D 323 " pdb=" CE MET D 323 " ideal model delta sinusoidal sigma weight residual 180.00 122.17 57.83 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 952 0.249 - 0.498: 0 0.498 - 0.747: 0 0.747 - 0.995: 0 0.995 - 1.244: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" C1 NAG D 905 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 905 " pdb=" O5 NAG D 905 " both_signs ideal model delta sigma weight residual False -2.40 -1.16 -1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN D 322 " pdb=" N ASN D 322 " pdb=" C ASN D 322 " pdb=" CB ASN D 322 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 950 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 905 " 0.245 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C7 NAG D 905 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 905 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG D 905 " -0.349 2.00e-02 2.50e+03 pdb=" O7 NAG D 905 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 903 " -0.247 2.00e-02 2.50e+03 2.08e-01 5.43e+02 pdb=" C7 NAG D 903 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG D 903 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG D 903 " 0.353 2.00e-02 2.50e+03 pdb=" O7 NAG D 903 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 904 " 0.054 2.00e-02 2.50e+03 4.46e-02 2.48e+01 pdb=" C7 NAG D 904 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 904 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG D 904 " -0.070 2.00e-02 2.50e+03 pdb=" O7 NAG D 904 " -0.009 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 75 2.63 - 3.20: 6069 3.20 - 3.76: 10152 3.76 - 4.33: 14209 4.33 - 4.90: 23577 Nonbonded interactions: 54082 Sorted by model distance: nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.059 2.440 nonbonded pdb=" O GLN D 388 " pdb=" NH1 ARG D 393 " model vdw 2.184 2.520 nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 902 " model vdw 2.186 2.230 nonbonded pdb=" O TYR D 515 " pdb=" OG1 THR D 519 " model vdw 2.249 2.440 nonbonded pdb=" OG SER D 331 " pdb=" O ILE D 358 " model vdw 2.250 2.440 ... (remaining 54077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 21.650 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.002 0.033 6666 Z= 0.148 Angle : 0.472 6.634 9060 Z= 0.252 Chirality : 0.056 1.244 953 Planarity : 0.009 0.210 1172 Dihedral : 13.058 89.215 2457 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % 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: -1.79 (0.27), residues: 789 helix: -0.48 (0.24), residues: 396 sheet: -1.57 (0.71), residues: 45 loop : -1.92 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 535 PHE 0.005 0.001 PHE A 515 TYR 0.007 0.001 TYR A 369 ARG 0.002 0.000 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8069 (p0) cc_final: 0.7819 (p0) REVERT: D 37 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6286 (mt-10) REVERT: D 94 LYS cc_start: 0.7854 (tttt) cc_final: 0.7561 (ttpp) REVERT: D 270 MET cc_start: 0.7896 (tpp) cc_final: 0.7637 (tpt) REVERT: D 294 THR cc_start: 0.6608 (p) cc_final: 0.6075 (p) REVERT: D 295 ASP cc_start: 0.6696 (p0) cc_final: 0.6268 (t0) REVERT: D 556 ASN cc_start: 0.7117 (m-40) cc_final: 0.6900 (m-40) REVERT: D 589 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6439 (tp30) REVERT: D 613 TYR cc_start: 0.6279 (p90) cc_final: 0.5932 (p90) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 1.2695 time to fit residues: 266.2204 Evaluate side-chains 150 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 33 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 360 ASN A 437 ASN A 439 ASN A 448 ASN A 460 ASN A 474 GLN A 481 ASN D 51 ASN D 58 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 101 GLN D 300 GLN D 373 HIS D 505 HIS D 522 GLN D 524 GLN D 578 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6666 Z= 0.201 Angle : 0.542 9.013 9060 Z= 0.276 Chirality : 0.042 0.147 953 Planarity : 0.004 0.031 1172 Dihedral : 3.778 28.317 929 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.45 % Allowed : 19.54 % Favored : 77.01 % 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: -0.47 (0.29), residues: 789 helix: 0.45 (0.26), residues: 403 sheet: -0.76 (0.77), residues: 45 loop : -1.11 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 203 HIS 0.006 0.001 HIS D 374 PHE 0.023 0.002 PHE D 555 TYR 0.017 0.001 TYR A 369 ARG 0.007 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.2725 (OUTLIER) cc_final: 0.2487 (p0) REVERT: A 405 ASN cc_start: 0.8289 (p0) cc_final: 0.7934 (p0) REVERT: D 216 ASP cc_start: 0.7254 (m-30) cc_final: 0.6974 (m-30) REVERT: D 270 MET cc_start: 0.7830 (tpp) cc_final: 0.7573 (tpt) REVERT: D 556 ASN cc_start: 0.7370 (m-40) cc_final: 0.7111 (m-40) REVERT: D 613 TYR cc_start: 0.6771 (p90) cc_final: 0.6328 (p90) outliers start: 24 outliers final: 10 residues processed: 169 average time/residue: 1.3704 time to fit residues: 243.8038 Evaluate side-chains 143 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 chunk 24 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 54 optimal weight: 0.3980 overall best weight: 0.1474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 239 HIS D 300 GLN D 345 HIS D 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6666 Z= 0.163 Angle : 0.509 8.858 9060 Z= 0.256 Chirality : 0.040 0.129 953 Planarity : 0.004 0.033 1172 Dihedral : 3.425 15.012 925 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 21.41 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 789 helix: 0.82 (0.26), residues: 404 sheet: -0.72 (0.74), residues: 45 loop : -0.88 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.014 0.001 PHE D 285 TYR 0.016 0.001 TYR A 369 ARG 0.004 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8204 (p0) cc_final: 0.7895 (p0) REVERT: D 114 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7385 (mmmt) REVERT: D 150 GLU cc_start: 0.7349 (tp30) cc_final: 0.7132 (tp30) REVERT: D 216 ASP cc_start: 0.7304 (m-30) cc_final: 0.7009 (m-30) REVERT: D 249 MET cc_start: 0.7681 (mpp) cc_final: 0.7375 (mmm) REVERT: D 270 MET cc_start: 0.7796 (tpp) cc_final: 0.7555 (tpt) REVERT: D 518 ARG cc_start: 0.7763 (tmm160) cc_final: 0.7446 (ppt90) REVERT: D 556 ASN cc_start: 0.7382 (m-40) cc_final: 0.7128 (m110) REVERT: D 613 TYR cc_start: 0.6887 (p90) cc_final: 0.6402 (p90) outliers start: 22 outliers final: 11 residues processed: 163 average time/residue: 1.1617 time to fit residues: 199.1611 Evaluate side-chains 154 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 76 optimal weight: 0.2980 chunk 68 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 477 ASN D 345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6666 Z= 0.163 Angle : 0.497 7.687 9060 Z= 0.249 Chirality : 0.040 0.127 953 Planarity : 0.004 0.032 1172 Dihedral : 3.378 12.861 925 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.30 % Allowed : 20.83 % Favored : 75.86 % 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: 0.26 (0.30), residues: 789 helix: 1.04 (0.27), residues: 399 sheet: -0.64 (0.73), residues: 45 loop : -0.68 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.017 0.001 PHE D 285 TYR 0.019 0.001 TYR D 50 ARG 0.004 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8200 (p0) cc_final: 0.7890 (p0) REVERT: D 43 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8716 (p) REVERT: D 216 ASP cc_start: 0.7366 (m-30) cc_final: 0.7043 (m-30) REVERT: D 270 MET cc_start: 0.7793 (tpp) cc_final: 0.7559 (tpp) REVERT: D 518 ARG cc_start: 0.7727 (tmm160) cc_final: 0.7454 (ppt90) REVERT: D 527 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6831 (tt0) REVERT: D 556 ASN cc_start: 0.7341 (m-40) cc_final: 0.7121 (m-40) REVERT: D 613 TYR cc_start: 0.6975 (p90) cc_final: 0.6449 (p90) outliers start: 23 outliers final: 8 residues processed: 174 average time/residue: 1.1217 time to fit residues: 205.6799 Evaluate side-chains 159 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 68 optimal weight: 0.0060 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 chunk 44 optimal weight: 0.0870 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 101 GLN D 330 ASN D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6666 Z= 0.137 Angle : 0.475 5.893 9060 Z= 0.238 Chirality : 0.039 0.124 953 Planarity : 0.003 0.031 1172 Dihedral : 3.219 12.107 925 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.59 % Allowed : 22.84 % Favored : 74.57 % 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: 0.51 (0.30), residues: 789 helix: 1.21 (0.27), residues: 399 sheet: -0.49 (0.73), residues: 45 loop : -0.52 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS D 374 PHE 0.018 0.001 PHE D 285 TYR 0.017 0.001 TYR A 369 ARG 0.003 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8166 (p0) cc_final: 0.7854 (p0) REVERT: A 408 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7810 (m) REVERT: D 216 ASP cc_start: 0.7380 (m-30) cc_final: 0.7119 (m-30) REVERT: D 270 MET cc_start: 0.7775 (tpp) cc_final: 0.7536 (tpp) REVERT: D 518 ARG cc_start: 0.7704 (tmm160) cc_final: 0.7497 (ppt90) REVERT: D 527 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6860 (tt0) REVERT: D 556 ASN cc_start: 0.7313 (m-40) cc_final: 0.7079 (m-40) REVERT: D 613 TYR cc_start: 0.6968 (p90) cc_final: 0.6484 (p90) outliers start: 18 outliers final: 9 residues processed: 170 average time/residue: 1.0875 time to fit residues: 195.1584 Evaluate side-chains 166 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 55 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN D 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6666 Z= 0.438 Angle : 0.632 10.097 9060 Z= 0.324 Chirality : 0.047 0.141 953 Planarity : 0.004 0.041 1172 Dihedral : 4.303 22.568 925 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.02 % Allowed : 22.27 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 789 helix: 0.89 (0.26), residues: 399 sheet: -0.49 (0.74), residues: 43 loop : -0.82 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 349 HIS 0.010 0.002 HIS D 374 PHE 0.026 0.002 PHE D 285 TYR 0.024 0.002 TYR D 50 ARG 0.004 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 368 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5676 (mm) REVERT: A 405 ASN cc_start: 0.8147 (p0) cc_final: 0.7896 (p0) REVERT: A 408 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7847 (m) REVERT: D 114 LYS cc_start: 0.7607 (mmmm) cc_final: 0.7281 (mmmm) REVERT: D 122 THR cc_start: 0.8337 (t) cc_final: 0.7969 (p) REVERT: D 216 ASP cc_start: 0.7455 (m-30) cc_final: 0.7154 (m-30) REVERT: D 270 MET cc_start: 0.7690 (tpp) cc_final: 0.7485 (tpp) REVERT: D 349 TRP cc_start: 0.8343 (m100) cc_final: 0.8122 (m100) REVERT: D 518 ARG cc_start: 0.7719 (tmm160) cc_final: 0.7500 (ttp80) REVERT: D 527 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6867 (tt0) REVERT: D 556 ASN cc_start: 0.7542 (m-40) cc_final: 0.7247 (m110) REVERT: D 613 TYR cc_start: 0.7374 (p90) cc_final: 0.6833 (p90) outliers start: 28 outliers final: 10 residues processed: 187 average time/residue: 1.1233 time to fit residues: 221.4612 Evaluate side-chains 170 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.1980 chunk 64 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 47 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN D 58 ASN D 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6666 Z= 0.209 Angle : 0.560 8.449 9060 Z= 0.280 Chirality : 0.041 0.128 953 Planarity : 0.004 0.036 1172 Dihedral : 3.876 16.274 925 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.44 % Allowed : 25.00 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 789 helix: 1.09 (0.27), residues: 398 sheet: -0.43 (0.75), residues: 43 loop : -0.66 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.024 0.001 PHE D 285 TYR 0.019 0.001 TYR D 50 ARG 0.005 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5614 (mm) REVERT: A 405 ASN cc_start: 0.8149 (p0) cc_final: 0.7843 (p0) REVERT: A 408 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7826 (m) REVERT: D 43 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8648 (p) REVERT: D 114 LYS cc_start: 0.7557 (mmmm) cc_final: 0.7255 (mmmm) REVERT: D 181 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6798 (mt-10) REVERT: D 216 ASP cc_start: 0.7427 (m-30) cc_final: 0.7118 (m-30) REVERT: D 270 MET cc_start: 0.7699 (tpp) cc_final: 0.7414 (tpp) REVERT: D 349 TRP cc_start: 0.8263 (m100) cc_final: 0.8038 (m100) REVERT: D 527 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6867 (tt0) REVERT: D 556 ASN cc_start: 0.7502 (m-40) cc_final: 0.7201 (m-40) REVERT: D 613 TYR cc_start: 0.7301 (p90) cc_final: 0.6763 (p90) outliers start: 17 outliers final: 10 residues processed: 178 average time/residue: 1.1500 time to fit residues: 214.9486 Evaluate side-chains 169 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 chunk 59 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 210 ASN D 300 GLN D 401 HIS D 508 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6666 Z= 0.322 Angle : 0.607 9.600 9060 Z= 0.307 Chirality : 0.044 0.136 953 Planarity : 0.004 0.035 1172 Dihedral : 4.175 18.403 925 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.73 % Allowed : 25.29 % Favored : 71.98 % 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 (0.30), residues: 789 helix: 0.98 (0.27), residues: 400 sheet: -0.42 (0.74), residues: 43 loop : -0.74 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 168 HIS 0.009 0.001 HIS D 374 PHE 0.026 0.002 PHE D 285 TYR 0.016 0.002 TYR A 369 ARG 0.009 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8149 (p0) cc_final: 0.7857 (p0) REVERT: A 408 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7825 (m) REVERT: D 37 GLU cc_start: 0.7028 (mp0) cc_final: 0.6784 (mp0) REVERT: D 114 LYS cc_start: 0.7573 (mmmm) cc_final: 0.7293 (mmmm) REVERT: D 216 ASP cc_start: 0.7443 (m-30) cc_final: 0.7172 (m-30) REVERT: D 270 MET cc_start: 0.7743 (tpp) cc_final: 0.7494 (tpp) REVERT: D 527 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6903 (tt0) REVERT: D 556 ASN cc_start: 0.7541 (m-40) cc_final: 0.7291 (m-40) REVERT: D 613 TYR cc_start: 0.7348 (p90) cc_final: 0.6797 (p90) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.9951 time to fit residues: 178.9632 Evaluate side-chains 166 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 445 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 21 optimal weight: 0.0870 chunk 64 optimal weight: 0.2980 chunk 67 optimal weight: 0.0870 chunk 70 optimal weight: 0.0000 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 52 optimal weight: 0.0770 overall best weight: 0.0696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN D 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6666 Z= 0.158 Angle : 0.538 7.176 9060 Z= 0.270 Chirality : 0.040 0.129 953 Planarity : 0.004 0.036 1172 Dihedral : 3.603 14.140 925 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.58 % Allowed : 26.58 % Favored : 71.84 % 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 (0.30), residues: 789 helix: 1.24 (0.27), residues: 395 sheet: -0.33 (0.75), residues: 43 loop : -0.60 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.022 0.001 PHE D 285 TYR 0.017 0.001 TYR A 369 ARG 0.008 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5590 (mm) REVERT: A 405 ASN cc_start: 0.8145 (p0) cc_final: 0.7809 (p0) REVERT: A 408 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7801 (m) REVERT: D 270 MET cc_start: 0.7783 (tpp) cc_final: 0.7533 (tpp) REVERT: D 556 ASN cc_start: 0.7511 (m-40) cc_final: 0.7250 (m-40) REVERT: D 613 TYR cc_start: 0.7278 (p90) cc_final: 0.6735 (p90) outliers start: 11 outliers final: 7 residues processed: 170 average time/residue: 1.2399 time to fit residues: 222.8395 Evaluate side-chains 165 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.0060 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6666 Z= 0.269 Angle : 0.601 9.182 9060 Z= 0.302 Chirality : 0.043 0.159 953 Planarity : 0.004 0.035 1172 Dihedral : 3.886 15.289 925 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.72 % Allowed : 27.16 % Favored : 71.12 % 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: 0.41 (0.30), residues: 789 helix: 1.20 (0.27), residues: 392 sheet: -0.29 (0.75), residues: 43 loop : -0.66 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 168 HIS 0.007 0.001 HIS D 374 PHE 0.027 0.002 PHE D 285 TYR 0.030 0.002 TYR D 50 ARG 0.008 0.001 ARG D 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5504 (mm) REVERT: A 405 ASN cc_start: 0.8131 (p0) cc_final: 0.7807 (p0) REVERT: A 408 SER cc_start: 0.8130 (OUTLIER) cc_final: 0.7836 (m) REVERT: D 527 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6867 (tt0) REVERT: D 556 ASN cc_start: 0.7530 (m-40) cc_final: 0.7306 (m-40) REVERT: D 613 TYR cc_start: 0.7347 (p90) cc_final: 0.6794 (p90) outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 1.0808 time to fit residues: 182.3835 Evaluate side-chains 157 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0570 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 64 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122853 restraints weight = 9059.079| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.96 r_work: 0.3460 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6666 Z= 0.245 Angle : 0.595 8.908 9060 Z= 0.300 Chirality : 0.043 0.166 953 Planarity : 0.004 0.036 1172 Dihedral : 3.863 15.885 925 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.16 % Allowed : 26.58 % Favored : 71.26 % 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: 0.34 (0.30), residues: 789 helix: 1.15 (0.27), residues: 392 sheet: -0.47 (0.73), residues: 43 loop : -0.70 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 168 HIS 0.006 0.001 HIS D 374 PHE 0.026 0.002 PHE D 285 TYR 0.017 0.001 TYR A 369 ARG 0.007 0.000 ARG D 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3941.23 seconds wall clock time: 71 minutes 15.01 seconds (4275.01 seconds total)