Starting phenix.real_space_refine on Mon Mar 11 06:31:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/03_2024/6uz2_20950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/03_2024/6uz2_20950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/03_2024/6uz2_20950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/03_2024/6uz2_20950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/03_2024/6uz2_20950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/03_2024/6uz2_20950.pdb" } resolution = 4.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4640 2.51 5 N 1328 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 325": "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: 7392 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3694 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'PTRANS': 13, 'TRANS': 556} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 749 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 21, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 434 Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3698 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 13, 'TRANS': 556} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 954 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 430 Time building chain proxies: 4.64, per 1000 atoms: 0.63 Number of scatterers: 7392 At special positions: 0 Unit cell: (72, 96, 131, 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 44 16.00 O 1380 8.00 N 1328 7.00 C 4640 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 71.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 24 through 47 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.574A pdb=" N ASP A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 62 through 109 removed outlier: 3.712A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 120 through 164 removed outlier: 3.556A pdb=" N GLY A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 196 Proline residue: A 176 - end of helix removed outlier: 3.755A pdb=" N MET A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 removed outlier: 5.028A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 269 removed outlier: 3.553A pdb=" N LYS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.640A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 280 through 324 Proline residue: A 297 - end of helix removed outlier: 4.073A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.834A pdb=" N ALA A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.687A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 527 Processing helix chain 'A' and resid 538 through 545 removed outlier: 4.118A pdb=" N ALA A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.521A pdb=" N ALA A 573 " --> pdb=" O GLY A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 22 Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 23 through 53 removed outlier: 3.861A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 60 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 120 through 164 Processing helix chain 'B' and resid 164 through 213 Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 275 removed outlier: 4.767A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 280 through 323 removed outlier: 3.632A pdb=" N PHE B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.797A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.668A pdb=" N ASN B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 527 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.677A pdb=" N LYS B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.590A pdb=" N GLN B 574 " --> pdb=" O GLY B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 5.615A pdb=" N ARG A 360 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 349 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 364 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ARG A 345 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 366 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU A 343 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 422 removed outlier: 5.311A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.653A pdb=" N VAL B 422 " --> pdb=" O ILE B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 586 hydrogen bonds defined for protein. 1734 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: 2.29 Time building geometry restraints manager: 3.57 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: 2498 1.34 - 1.45: 996 1.45 - 1.57: 3894 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 7474 Sorted by residual: bond pdb=" CG ARG B 296 " pdb=" CD ARG B 296 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.15e+00 bond pdb=" CB TRP A 17 " pdb=" CG TRP A 17 " ideal model delta sigma weight residual 1.498 1.436 0.062 3.10e-02 1.04e+03 4.02e+00 bond pdb=" CB PHE A 13 " pdb=" CG PHE A 13 " ideal model delta sigma weight residual 1.502 1.459 0.043 2.30e-02 1.89e+03 3.52e+00 bond pdb=" CB TRP B 17 " pdb=" CG TRP B 17 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.30e+00 ... (remaining 7469 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.43: 120 105.43 - 112.58: 4184 112.58 - 119.73: 2254 119.73 - 126.88: 3589 126.88 - 134.03: 48 Bond angle restraints: 10195 Sorted by residual: angle pdb=" N HIS B 537 " pdb=" CA HIS B 537 " pdb=" C HIS B 537 " ideal model delta sigma weight residual 112.59 100.04 12.55 1.22e+00 6.72e-01 1.06e+02 angle pdb=" C MET A 295 " pdb=" N ARG A 296 " pdb=" CA ARG A 296 " ideal model delta sigma weight residual 119.83 112.91 6.92 1.11e+00 8.12e-01 3.88e+01 angle pdb=" N ALA B 536 " pdb=" CA ALA B 536 " pdb=" C ALA B 536 " ideal model delta sigma weight residual 108.56 118.02 -9.46 1.74e+00 3.30e-01 2.95e+01 angle pdb=" N SER B 164 " pdb=" CA SER B 164 " pdb=" C SER B 164 " ideal model delta sigma weight residual 107.93 116.15 -8.22 1.65e+00 3.67e-01 2.48e+01 angle pdb=" N TYR A 163 " pdb=" CA TYR A 163 " pdb=" C TYR A 163 " ideal model delta sigma weight residual 111.36 116.32 -4.96 1.09e+00 8.42e-01 2.07e+01 ... (remaining 10190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.39: 3904 13.39 - 26.77: 398 26.77 - 40.16: 121 40.16 - 53.54: 39 53.54 - 66.93: 9 Dihedral angle restraints: 4471 sinusoidal: 1189 harmonic: 3282 Sorted by residual: dihedral pdb=" CA GLU A 552 " pdb=" C GLU A 552 " pdb=" N ASP A 553 " pdb=" CA ASP A 553 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA A 457 " pdb=" C ALA A 457 " pdb=" N TYR A 458 " pdb=" CA TYR A 458 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS B 544 " pdb=" C LYS B 544 " pdb=" N ALA B 545 " pdb=" CA ALA B 545 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 883 0.048 - 0.096: 318 0.096 - 0.143: 73 0.143 - 0.191: 5 0.191 - 0.239: 5 Chirality restraints: 1284 Sorted by residual: chirality pdb=" CA VAL A 334 " pdb=" N VAL A 334 " pdb=" C VAL A 334 " pdb=" CB VAL A 334 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ALA B 536 " pdb=" N ALA B 536 " pdb=" C ALA B 536 " pdb=" CB ALA B 536 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA TYR A 163 " pdb=" N TYR A 163 " pdb=" C TYR A 163 " pdb=" CB TYR A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1281 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 262 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ALA B 262 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA B 262 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 263 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 136 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ALA B 136 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA B 136 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 137 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 296 " 0.039 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO B 297 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.032 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1320 2.74 - 3.28: 8957 3.28 - 3.82: 12479 3.82 - 4.36: 13927 4.36 - 4.90: 22048 Nonbonded interactions: 58731 Sorted by model distance: nonbonded pdb=" O ARG A 78 " pdb=" OG1 THR A 81 " model vdw 2.197 2.440 nonbonded pdb=" O GLN B 256 " pdb=" OG SER B 260 " model vdw 2.200 2.440 nonbonded pdb=" O PRO A 297 " pdb=" OG SER A 300 " model vdw 2.201 2.440 nonbonded pdb=" O ALA A 175 " pdb=" OG SER A 179 " model vdw 2.202 2.440 nonbonded pdb=" O VAL A 135 " pdb=" OG SER A 139 " model vdw 2.208 2.440 ... (remaining 58726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 580)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.990 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.950 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.009 0.068 7474 Z= 0.574 Angle : 1.131 13.667 10195 Z= 0.668 Chirality : 0.051 0.239 1284 Planarity : 0.005 0.057 1327 Dihedral : 13.781 66.927 2339 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.49 % Favored : 84.33 % Rotamer: Outliers : 2.00 % Allowed : 12.70 % Favored : 85.30 % 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: -5.29 (0.18), residues: 1136 helix: -3.00 (0.14), residues: 715 sheet: -3.18 (0.60), residues: 43 loop : -4.28 (0.25), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 91 HIS 0.009 0.002 HIS A 107 PHE 0.040 0.004 PHE A 308 TYR 0.010 0.002 TYR A 83 ARG 0.005 0.001 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8540 (tptm) cc_final: 0.8238 (pttt) REVERT: A 148 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7782 (tpp80) REVERT: A 159 MET cc_start: 0.9199 (mmm) cc_final: 0.8523 (mmm) REVERT: A 189 PHE cc_start: 0.8718 (m-10) cc_final: 0.8247 (m-80) REVERT: A 190 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8771 (mmp80) REVERT: A 196 MET cc_start: 0.9023 (mmm) cc_final: 0.8645 (mmm) REVERT: A 198 ASN cc_start: 0.9149 (m-40) cc_final: 0.8784 (p0) REVERT: A 208 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8117 (mm-30) REVERT: A 210 MET cc_start: 0.8939 (mmm) cc_final: 0.8543 (mtt) REVERT: A 212 LYS cc_start: 0.9177 (mttt) cc_final: 0.8634 (mttm) REVERT: A 230 PHE cc_start: 0.8652 (m-10) cc_final: 0.8355 (m-10) REVERT: A 296 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5146 (ttm170) REVERT: B 98 MET cc_start: 0.9275 (ttm) cc_final: 0.8646 (tpp) REVERT: B 171 LEU cc_start: 0.9173 (mt) cc_final: 0.8938 (mt) REVERT: B 189 PHE cc_start: 0.8602 (m-10) cc_final: 0.8196 (t80) REVERT: B 190 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8715 (ptt180) REVERT: B 191 ASN cc_start: 0.8431 (m-40) cc_final: 0.8061 (t0) REVERT: B 196 MET cc_start: 0.8861 (mmm) cc_final: 0.8567 (tpp) REVERT: B 210 MET cc_start: 0.8608 (tpt) cc_final: 0.8363 (tpt) REVERT: B 296 ARG cc_start: 0.5595 (mtt180) cc_final: 0.4564 (ttm170) REVERT: B 312 MET cc_start: 0.9242 (mmm) cc_final: 0.9026 (mmm) outliers start: 11 outliers final: 5 residues processed: 252 average time/residue: 0.1881 time to fit residues: 63.1542 Evaluate side-chains 189 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 0.0000 chunk 54 optimal weight: 50.0000 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 30.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7474 Z= 0.232 Angle : 0.694 9.844 10195 Z= 0.370 Chirality : 0.045 0.142 1284 Planarity : 0.004 0.051 1327 Dihedral : 5.420 23.967 1184 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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: -2.67 (0.23), residues: 1136 helix: -0.91 (0.17), residues: 750 sheet: -3.13 (0.76), residues: 39 loop : -3.38 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 91 HIS 0.008 0.004 HIS A 107 PHE 0.038 0.003 PHE A 115 TYR 0.014 0.002 TYR A 268 ARG 0.004 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 0.939 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: A 56 PHE cc_start: 0.8089 (m-80) cc_final: 0.7875 (m-80) REVERT: A 63 VAL cc_start: 0.9299 (p) cc_final: 0.8974 (m) REVERT: A 118 LYS cc_start: 0.8184 (tptm) cc_final: 0.7946 (pttt) REVERT: A 131 ASP cc_start: 0.8707 (m-30) cc_final: 0.8361 (m-30) REVERT: A 159 MET cc_start: 0.9147 (mmm) cc_final: 0.7802 (mmm) REVERT: A 171 LEU cc_start: 0.8978 (mt) cc_final: 0.8742 (mt) REVERT: A 198 ASN cc_start: 0.9112 (m-40) cc_final: 0.8730 (p0) REVERT: A 212 LYS cc_start: 0.9092 (mttt) cc_final: 0.8886 (mttm) REVERT: A 216 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8840 (pt0) REVERT: A 230 PHE cc_start: 0.8363 (m-10) cc_final: 0.7498 (m-10) REVERT: A 323 ASP cc_start: 0.8923 (m-30) cc_final: 0.8639 (m-30) REVERT: B 36 LEU cc_start: 0.9330 (mt) cc_final: 0.8921 (tt) REVERT: B 54 ASP cc_start: 0.8243 (m-30) cc_final: 0.7375 (m-30) REVERT: B 75 MET cc_start: 0.8871 (mmt) cc_final: 0.8576 (mmm) REVERT: B 98 MET cc_start: 0.9138 (ttm) cc_final: 0.8330 (tpp) REVERT: B 105 PHE cc_start: 0.8407 (m-10) cc_final: 0.7812 (m-10) REVERT: B 159 MET cc_start: 0.8970 (mmm) cc_final: 0.8668 (mmm) REVERT: B 190 ARG cc_start: 0.8977 (mtt180) cc_final: 0.8619 (ptt180) REVERT: B 191 ASN cc_start: 0.8230 (m-40) cc_final: 0.8000 (t0) REVERT: B 214 HIS cc_start: 0.8025 (p-80) cc_final: 0.7801 (p-80) REVERT: B 230 PHE cc_start: 0.8371 (m-10) cc_final: 0.7691 (m-10) REVERT: B 261 LEU cc_start: 0.9281 (mt) cc_final: 0.8866 (tp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1659 time to fit residues: 59.2671 Evaluate side-chains 200 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 102 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7474 Z= 0.343 Angle : 0.740 11.621 10195 Z= 0.395 Chirality : 0.045 0.187 1284 Planarity : 0.004 0.052 1327 Dihedral : 5.162 20.701 1184 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.36 % Allowed : 5.81 % Favored : 93.83 % 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: -1.92 (0.24), residues: 1136 helix: -0.33 (0.18), residues: 765 sheet: -2.21 (0.73), residues: 44 loop : -3.31 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 66 HIS 0.005 0.002 HIS A 107 PHE 0.059 0.003 PHE A 105 TYR 0.029 0.003 TYR A 87 ARG 0.003 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 0.923 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: A 118 LYS cc_start: 0.8267 (tptm) cc_final: 0.7995 (pttt) REVERT: A 131 ASP cc_start: 0.8801 (m-30) cc_final: 0.8512 (m-30) REVERT: A 171 LEU cc_start: 0.9012 (mt) cc_final: 0.8798 (mt) REVERT: A 210 MET cc_start: 0.8724 (mtp) cc_final: 0.8502 (ttt) REVERT: A 212 LYS cc_start: 0.8948 (mttt) cc_final: 0.8658 (tppt) REVERT: A 323 ASP cc_start: 0.9089 (m-30) cc_final: 0.8720 (m-30) REVERT: B 53 ASP cc_start: 0.8208 (p0) cc_final: 0.7833 (p0) REVERT: B 75 MET cc_start: 0.8902 (mmt) cc_final: 0.8668 (mmm) REVERT: B 98 MET cc_start: 0.9198 (ttm) cc_final: 0.8398 (tpp) REVERT: B 159 MET cc_start: 0.9125 (mmm) cc_final: 0.8778 (mmm) REVERT: B 190 ARG cc_start: 0.9029 (mtt180) cc_final: 0.8552 (ptt180) REVERT: B 191 ASN cc_start: 0.8213 (m-40) cc_final: 0.7858 (t0) REVERT: B 196 MET cc_start: 0.7961 (tpt) cc_final: 0.7674 (tpp) REVERT: B 200 MET cc_start: 0.8458 (mtm) cc_final: 0.8014 (mtm) REVERT: B 240 GLN cc_start: 0.8989 (mt0) cc_final: 0.8722 (mt0) REVERT: B 296 ARG cc_start: 0.5833 (ttm170) cc_final: 0.5515 (ttm170) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.1602 time to fit residues: 51.0008 Evaluate side-chains 188 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7474 Z= 0.315 Angle : 0.692 10.059 10195 Z= 0.370 Chirality : 0.044 0.158 1284 Planarity : 0.004 0.050 1327 Dihedral : 4.918 20.154 1184 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 0.18 % Allowed : 5.44 % Favored : 94.37 % 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: -1.36 (0.25), residues: 1136 helix: 0.12 (0.18), residues: 763 sheet: -2.37 (0.90), residues: 32 loop : -3.09 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 66 HIS 0.002 0.001 HIS A 107 PHE 0.034 0.003 PHE A 105 TYR 0.013 0.001 TYR A 268 ARG 0.004 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8334 (t80) cc_final: 0.8091 (t80) REVERT: A 118 LYS cc_start: 0.8302 (tptm) cc_final: 0.7965 (pttt) REVERT: A 131 ASP cc_start: 0.8694 (m-30) cc_final: 0.8474 (m-30) REVERT: A 171 LEU cc_start: 0.8945 (mt) cc_final: 0.8698 (mt) REVERT: A 189 PHE cc_start: 0.8816 (m-10) cc_final: 0.8442 (m-80) REVERT: A 208 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 210 MET cc_start: 0.8617 (mtp) cc_final: 0.8073 (ttt) REVERT: A 212 LYS cc_start: 0.8869 (mttt) cc_final: 0.8652 (tppt) REVERT: A 226 GLU cc_start: 0.8667 (tp30) cc_final: 0.7477 (tp30) REVERT: A 230 PHE cc_start: 0.8474 (m-10) cc_final: 0.8008 (m-10) REVERT: B 53 ASP cc_start: 0.8318 (p0) cc_final: 0.7704 (p0) REVERT: B 54 ASP cc_start: 0.7997 (m-30) cc_final: 0.7390 (m-30) REVERT: B 75 MET cc_start: 0.8784 (mmt) cc_final: 0.8537 (mmm) REVERT: B 98 MET cc_start: 0.9122 (ttt) cc_final: 0.8377 (tmm) REVERT: B 125 LEU cc_start: 0.9317 (tt) cc_final: 0.8947 (tt) REVERT: B 160 MET cc_start: 0.8960 (mmm) cc_final: 0.8611 (mmm) REVERT: B 171 LEU cc_start: 0.9062 (mt) cc_final: 0.8853 (mt) REVERT: B 190 ARG cc_start: 0.9006 (mtt180) cc_final: 0.8497 (ptt180) REVERT: B 196 MET cc_start: 0.8015 (tpt) cc_final: 0.7308 (tpp) REVERT: B 200 MET cc_start: 0.8553 (mtm) cc_final: 0.7699 (mtm) REVERT: B 240 GLN cc_start: 0.8967 (mt0) cc_final: 0.8611 (tt0) REVERT: B 296 ARG cc_start: 0.5528 (ttm170) cc_final: 0.5124 (ttm170) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1449 time to fit residues: 46.1861 Evaluate side-chains 187 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 40.0000 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 27 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7474 Z= 0.317 Angle : 0.699 9.440 10195 Z= 0.374 Chirality : 0.045 0.141 1284 Planarity : 0.004 0.051 1327 Dihedral : 4.829 19.314 1184 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1136 helix: 0.44 (0.19), residues: 750 sheet: -3.88 (0.80), residues: 25 loop : -2.73 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 66 HIS 0.006 0.002 HIS A 107 PHE 0.034 0.003 PHE A 105 TYR 0.017 0.002 TYR B 163 ARG 0.003 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 0.917 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: A 118 LYS cc_start: 0.8334 (tptm) cc_final: 0.8014 (pttt) REVERT: A 131 ASP cc_start: 0.8743 (m-30) cc_final: 0.8535 (m-30) REVERT: A 159 MET cc_start: 0.9228 (mmm) cc_final: 0.8946 (mmm) REVERT: A 189 PHE cc_start: 0.8802 (m-10) cc_final: 0.8500 (m-80) REVERT: A 191 ASN cc_start: 0.8282 (m-40) cc_final: 0.7745 (t0) REVERT: A 208 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8518 (mm-30) REVERT: A 212 LYS cc_start: 0.8962 (mttt) cc_final: 0.8690 (tppt) REVERT: A 230 PHE cc_start: 0.8412 (m-10) cc_final: 0.8156 (m-10) REVERT: A 323 ASP cc_start: 0.9092 (m-30) cc_final: 0.8762 (m-30) REVERT: B 98 MET cc_start: 0.9153 (ttt) cc_final: 0.8049 (tpp) REVERT: B 159 MET cc_start: 0.8943 (tpt) cc_final: 0.8666 (mmm) REVERT: B 160 MET cc_start: 0.8980 (mmm) cc_final: 0.8580 (mmm) REVERT: B 171 LEU cc_start: 0.9055 (mt) cc_final: 0.8840 (mt) REVERT: B 190 ARG cc_start: 0.9084 (mtt180) cc_final: 0.8521 (ptt180) REVERT: B 196 MET cc_start: 0.7774 (tpt) cc_final: 0.7258 (tpp) REVERT: B 240 GLN cc_start: 0.8981 (mt0) cc_final: 0.8772 (tt0) REVERT: B 296 ARG cc_start: 0.5096 (ttm170) cc_final: 0.4780 (ttm170) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1486 time to fit residues: 47.4073 Evaluate side-chains 186 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.0670 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7474 Z= 0.199 Angle : 0.638 10.623 10195 Z= 0.330 Chirality : 0.044 0.140 1284 Planarity : 0.003 0.041 1327 Dihedral : 4.439 19.574 1184 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1136 helix: 0.85 (0.19), residues: 763 sheet: -2.93 (0.63), residues: 45 loop : -2.54 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 66 HIS 0.004 0.001 HIS A 214 PHE 0.025 0.002 PHE A 23 TYR 0.012 0.001 TYR B 87 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9052 (m-80) cc_final: 0.8616 (m-80) REVERT: A 118 LYS cc_start: 0.8065 (tptm) cc_final: 0.7851 (pttt) REVERT: A 189 PHE cc_start: 0.8366 (m-10) cc_final: 0.8032 (m-80) REVERT: A 191 ASN cc_start: 0.8203 (m-40) cc_final: 0.7734 (t0) REVERT: A 192 ILE cc_start: 0.8992 (mt) cc_final: 0.8628 (mt) REVERT: A 208 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 212 LYS cc_start: 0.8983 (mttt) cc_final: 0.8580 (tppt) REVERT: A 288 PHE cc_start: 0.8974 (m-80) cc_final: 0.8698 (m-80) REVERT: A 296 ARG cc_start: 0.5667 (ttt180) cc_final: 0.5293 (ttt180) REVERT: A 323 ASP cc_start: 0.8964 (m-30) cc_final: 0.8756 (m-30) REVERT: B 53 ASP cc_start: 0.8156 (p0) cc_final: 0.7581 (p0) REVERT: B 54 ASP cc_start: 0.7930 (m-30) cc_final: 0.7280 (m-30) REVERT: B 75 MET cc_start: 0.8692 (mmt) cc_final: 0.8485 (mmm) REVERT: B 80 ILE cc_start: 0.9362 (tt) cc_final: 0.9118 (mm) REVERT: B 98 MET cc_start: 0.9161 (ttt) cc_final: 0.7812 (tpp) REVERT: B 160 MET cc_start: 0.8905 (mmm) cc_final: 0.8659 (mmm) REVERT: B 190 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8454 (ptt180) REVERT: B 196 MET cc_start: 0.7240 (tpt) cc_final: 0.6940 (tpt) REVERT: B 240 GLN cc_start: 0.8914 (mt0) cc_final: 0.8614 (tt0) REVERT: B 296 ARG cc_start: 0.5280 (ttm170) cc_final: 0.4830 (ttm170) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1496 time to fit residues: 51.3744 Evaluate side-chains 196 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 50.0000 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7474 Z= 0.217 Angle : 0.648 9.471 10195 Z= 0.339 Chirality : 0.044 0.170 1284 Planarity : 0.003 0.038 1327 Dihedral : 4.310 17.218 1184 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1136 helix: 0.98 (0.19), residues: 772 sheet: -2.86 (0.61), residues: 50 loop : -2.51 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 66 HIS 0.005 0.002 HIS A 214 PHE 0.047 0.002 PHE A 105 TYR 0.010 0.001 TYR B 87 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9041 (m-80) cc_final: 0.8591 (m-80) REVERT: A 171 LEU cc_start: 0.8786 (mt) cc_final: 0.8574 (mt) REVERT: A 189 PHE cc_start: 0.8279 (m-10) cc_final: 0.7834 (m-80) REVERT: A 191 ASN cc_start: 0.8236 (m-40) cc_final: 0.7809 (t0) REVERT: A 212 LYS cc_start: 0.9061 (mttt) cc_final: 0.8588 (tppt) REVERT: A 226 GLU cc_start: 0.8228 (tp30) cc_final: 0.6937 (tp30) REVERT: A 288 PHE cc_start: 0.8953 (m-80) cc_final: 0.8746 (m-80) REVERT: A 296 ARG cc_start: 0.5312 (ttt180) cc_final: 0.4878 (ttt180) REVERT: A 298 LEU cc_start: 0.9136 (mt) cc_final: 0.8880 (mt) REVERT: A 323 ASP cc_start: 0.9087 (m-30) cc_final: 0.8880 (m-30) REVERT: B 53 ASP cc_start: 0.8102 (p0) cc_final: 0.7459 (p0) REVERT: B 54 ASP cc_start: 0.7884 (m-30) cc_final: 0.7167 (m-30) REVERT: B 75 MET cc_start: 0.8671 (mmt) cc_final: 0.8409 (mmm) REVERT: B 98 MET cc_start: 0.9152 (ttt) cc_final: 0.7724 (tpp) REVERT: B 149 GLU cc_start: 0.8396 (mp0) cc_final: 0.7516 (mp0) REVERT: B 160 MET cc_start: 0.8918 (mmm) cc_final: 0.8659 (mmm) REVERT: B 171 LEU cc_start: 0.8965 (mt) cc_final: 0.8706 (mt) REVERT: B 190 ARG cc_start: 0.9084 (mtt180) cc_final: 0.8523 (ptt180) REVERT: B 240 GLN cc_start: 0.8805 (mt0) cc_final: 0.8557 (mt0) REVERT: B 261 LEU cc_start: 0.9305 (mt) cc_final: 0.8781 (tp) REVERT: B 296 ARG cc_start: 0.5314 (ttm170) cc_final: 0.4869 (ttm170) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1471 time to fit residues: 47.6808 Evaluate side-chains 189 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 40.0000 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.0170 chunk 54 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN B 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7474 Z= 0.185 Angle : 0.631 11.305 10195 Z= 0.323 Chirality : 0.043 0.157 1284 Planarity : 0.003 0.037 1327 Dihedral : 4.155 16.654 1184 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.05 (0.27), residues: 1136 helix: 1.10 (0.19), residues: 783 sheet: -2.76 (0.62), residues: 50 loop : -2.30 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 66 HIS 0.008 0.003 HIS A 107 PHE 0.032 0.002 PHE A 105 TYR 0.013 0.001 TYR B 87 ARG 0.003 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.914 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: A 43 PHE cc_start: 0.9085 (m-80) cc_final: 0.8655 (m-80) REVERT: A 105 PHE cc_start: 0.8059 (m-80) cc_final: 0.7686 (m-10) REVERT: A 125 LEU cc_start: 0.9060 (tt) cc_final: 0.8795 (pt) REVERT: A 171 LEU cc_start: 0.8783 (mt) cc_final: 0.8490 (mt) REVERT: A 189 PHE cc_start: 0.8112 (m-10) cc_final: 0.7721 (m-80) REVERT: A 191 ASN cc_start: 0.8204 (m-40) cc_final: 0.7802 (t0) REVERT: A 212 LYS cc_start: 0.9063 (mttt) cc_final: 0.8713 (tppt) REVERT: A 294 LEU cc_start: 0.9273 (tp) cc_final: 0.9068 (tp) REVERT: A 296 ARG cc_start: 0.5373 (ttt180) cc_final: 0.4830 (ttt180) REVERT: A 298 LEU cc_start: 0.9170 (mt) cc_final: 0.8873 (mt) REVERT: B 53 ASP cc_start: 0.7918 (p0) cc_final: 0.7627 (p0) REVERT: B 75 MET cc_start: 0.8680 (mmt) cc_final: 0.8458 (mmm) REVERT: B 98 MET cc_start: 0.9202 (ttt) cc_final: 0.7791 (tpp) REVERT: B 111 MET cc_start: 0.7297 (ttt) cc_final: 0.6775 (tmm) REVERT: B 131 ASP cc_start: 0.8177 (m-30) cc_final: 0.7930 (m-30) REVERT: B 133 GLU cc_start: 0.8885 (tp30) cc_final: 0.8665 (mm-30) REVERT: B 160 MET cc_start: 0.8840 (mmm) cc_final: 0.8600 (mmm) REVERT: B 171 LEU cc_start: 0.8911 (mt) cc_final: 0.8660 (mt) REVERT: B 190 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8448 (ptt180) REVERT: B 240 GLN cc_start: 0.8720 (mt0) cc_final: 0.8514 (mt0) REVERT: B 261 LEU cc_start: 0.9237 (mt) cc_final: 0.8734 (tp) REVERT: B 296 ARG cc_start: 0.5190 (ttm170) cc_final: 0.4806 (ttm170) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1544 time to fit residues: 52.2510 Evaluate side-chains 198 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 40.0000 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7474 Z= 0.247 Angle : 0.672 12.150 10195 Z= 0.353 Chirality : 0.044 0.180 1284 Planarity : 0.003 0.035 1327 Dihedral : 4.224 19.231 1184 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1136 helix: 1.05 (0.19), residues: 782 sheet: -2.69 (0.63), residues: 50 loop : -2.32 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 66 HIS 0.009 0.003 HIS A 107 PHE 0.051 0.003 PHE B 105 TYR 0.010 0.001 TYR A 87 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9100 (m-80) cc_final: 0.8613 (m-10) REVERT: A 131 ASP cc_start: 0.8625 (m-30) cc_final: 0.8229 (m-30) REVERT: A 171 LEU cc_start: 0.8810 (mt) cc_final: 0.8562 (mt) REVERT: A 189 PHE cc_start: 0.8224 (m-10) cc_final: 0.7821 (m-80) REVERT: A 191 ASN cc_start: 0.8218 (m-40) cc_final: 0.7832 (t0) REVERT: A 212 LYS cc_start: 0.8966 (mttt) cc_final: 0.8677 (tppt) REVERT: A 296 ARG cc_start: 0.5346 (ttt180) cc_final: 0.5015 (ttt180) REVERT: A 298 LEU cc_start: 0.9188 (mt) cc_final: 0.8945 (mt) REVERT: B 53 ASP cc_start: 0.8015 (p0) cc_final: 0.7303 (p0) REVERT: B 54 ASP cc_start: 0.7731 (m-30) cc_final: 0.7183 (m-30) REVERT: B 98 MET cc_start: 0.9241 (ttt) cc_final: 0.7824 (tpp) REVERT: B 111 MET cc_start: 0.7263 (ttt) cc_final: 0.6748 (tmm) REVERT: B 149 GLU cc_start: 0.8276 (mp0) cc_final: 0.7491 (mp0) REVERT: B 160 MET cc_start: 0.8843 (mmm) cc_final: 0.8618 (mmp) REVERT: B 171 LEU cc_start: 0.8984 (mt) cc_final: 0.8697 (mt) REVERT: B 190 ARG cc_start: 0.9116 (mtt180) cc_final: 0.8563 (ptt180) REVERT: B 240 GLN cc_start: 0.8812 (mt0) cc_final: 0.8584 (mt0) REVERT: B 261 LEU cc_start: 0.9296 (mt) cc_final: 0.8778 (tp) REVERT: B 296 ARG cc_start: 0.5305 (ttm170) cc_final: 0.4754 (ttm170) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1486 time to fit residues: 48.9832 Evaluate side-chains 190 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7474 Z= 0.232 Angle : 0.668 10.855 10195 Z= 0.344 Chirality : 0.044 0.170 1284 Planarity : 0.003 0.036 1327 Dihedral : 4.177 17.988 1184 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.09 (0.27), residues: 1136 helix: 1.11 (0.19), residues: 776 sheet: -2.35 (0.66), residues: 55 loop : -2.20 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 66 HIS 0.007 0.002 HIS A 214 PHE 0.041 0.003 PHE B 105 TYR 0.014 0.001 TYR A 87 ARG 0.004 0.000 ARG A 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9135 (m-80) cc_final: 0.8637 (m-10) REVERT: A 131 ASP cc_start: 0.8519 (m-30) cc_final: 0.8158 (m-30) REVERT: A 171 LEU cc_start: 0.8834 (mt) cc_final: 0.8590 (mt) REVERT: A 189 PHE cc_start: 0.8201 (m-10) cc_final: 0.7831 (m-80) REVERT: A 191 ASN cc_start: 0.8220 (m-40) cc_final: 0.7811 (t0) REVERT: A 212 LYS cc_start: 0.8922 (mttt) cc_final: 0.8669 (tppt) REVERT: A 257 LEU cc_start: 0.9219 (tp) cc_final: 0.9002 (tp) REVERT: A 294 LEU cc_start: 0.9357 (tp) cc_final: 0.9123 (tp) REVERT: A 296 ARG cc_start: 0.5414 (ttt180) cc_final: 0.4798 (ttt180) REVERT: A 298 LEU cc_start: 0.9216 (mt) cc_final: 0.8911 (mt) REVERT: B 53 ASP cc_start: 0.7857 (p0) cc_final: 0.7567 (p0) REVERT: B 98 MET cc_start: 0.9237 (ttt) cc_final: 0.7808 (tpp) REVERT: B 111 MET cc_start: 0.7172 (ttt) cc_final: 0.6563 (tmm) REVERT: B 130 TYR cc_start: 0.8568 (t80) cc_final: 0.8353 (t80) REVERT: B 160 MET cc_start: 0.8799 (mmm) cc_final: 0.8519 (mmm) REVERT: B 171 LEU cc_start: 0.8989 (mt) cc_final: 0.8733 (mt) REVERT: B 190 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8495 (ptt180) REVERT: B 240 GLN cc_start: 0.8622 (mt0) cc_final: 0.8389 (tt0) REVERT: B 261 LEU cc_start: 0.9284 (mt) cc_final: 0.8779 (tp) REVERT: B 296 ARG cc_start: 0.5183 (ttm170) cc_final: 0.4885 (ttm170) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1455 time to fit residues: 48.4351 Evaluate side-chains 190 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.115560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089624 restraints weight = 23421.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.091924 restraints weight = 15308.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093559 restraints weight = 11061.567| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7474 Z= 0.196 Angle : 0.654 12.157 10195 Z= 0.332 Chirality : 0.044 0.164 1284 Planarity : 0.003 0.037 1327 Dihedral : 4.089 18.564 1184 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.21 (0.27), residues: 1136 helix: 1.22 (0.19), residues: 772 sheet: -2.31 (0.66), residues: 55 loop : -2.16 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 66 HIS 0.007 0.002 HIS A 214 PHE 0.033 0.002 PHE B 230 TYR 0.012 0.001 TYR B 87 ARG 0.004 0.000 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1741.52 seconds wall clock time: 32 minutes 2.89 seconds (1922.89 seconds total)