Starting phenix.real_space_refine on Tue Jul 23 15:54:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/07_2024/8qz8_18772_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/07_2024/8qz8_18772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/07_2024/8qz8_18772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/07_2024/8qz8_18772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/07_2024/8qz8_18772_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/07_2024/8qz8_18772_neut.cif" } resolution = 3.13 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= 0.002 sd= 0.072 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7113 2.51 5 N 2035 2.21 5 O 2292 1.98 5 H 11077 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 22629 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7910 Classifications: {'peptide': 512} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 491} Chain breaks: 1 Chain: "C" Number of atoms: 6696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6696 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain: "V" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1046 Classifications: {'RNA': 33} Modifications used: {'3*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 17, 'rna3p': 15} Chain breaks: 1 Chain: "P" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Classifications: {'RNA': 9} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 47.930 47.016 19.706 1.00 76.37 S ATOM 4473 SG CYS A 282 45.639 45.224 17.052 1.00 87.29 S ATOM 18195 SG CYS C 233 21.177 52.353 108.814 1.00129.37 S ATOM 18219 SG CYS C 235 21.445 54.226 105.382 1.00120.87 S ATOM 16861 SG CYS C 146 9.859 61.301 88.729 1.00133.35 S ATOM 17049 SG CYS C 159 9.623 64.497 90.979 1.00131.26 S ATOM 17105 SG CYS C 163 12.623 62.252 91.247 1.00119.92 S ATOM 17115 SG CYS C 164 12.238 64.813 88.738 1.00123.42 S Time building chain proxies: 10.81, per 1000 atoms: 0.48 Number of scatterers: 22629 At special positions: 0 Unit cell: (92.19, 101.848, 125.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 45 15.00 Mg 1 11.99 O 2292 8.00 N 2035 7.00 C 7113 6.00 H 11077 1.00 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: 18.39 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " Number of angles added : 8 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 41.7% alpha, 14.0% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 10.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.538A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.665A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.936A pdb=" N THR A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.901A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.733A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.567A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.660A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 4.020A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 236 through 248 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.687A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.607A pdb=" N SER B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.894A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.534A pdb=" N PHE C 8 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.655A pdb=" N SER C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.415A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.663A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.632A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.614A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 202 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.614A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 202 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 160 removed outlier: 7.072A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 479 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 81 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.943A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388 removed outlier: 3.614A pdb=" N THR C 385 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 8.46 Time building geometry restraints manager: 18.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11045 1.04 - 1.24: 1512 1.24 - 1.44: 3735 1.44 - 1.65: 6568 1.65 - 1.85: 90 Bond restraints: 22950 Sorted by residual: bond pdb=" CB CYS C 146 " pdb=" SG CYS C 146 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.37e-01 bond pdb=" C3' A V 29 " pdb=" O3' A V 29 " ideal model delta sigma weight residual 1.427 1.440 -0.013 1.50e-02 4.44e+03 7.70e-01 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.51e-02 4.39e+03 7.57e-01 bond pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 1.471 1.456 0.015 1.74e-02 3.30e+03 7.30e-01 bond pdb=" CB CYS C 146 " pdb=" HB2 CYS C 146 " ideal model delta sigma weight residual 0.970 0.953 0.017 2.00e-02 2.50e+03 7.16e-01 ... (remaining 22945 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.89: 427 105.89 - 112.92: 26520 112.92 - 119.95: 6298 119.95 - 126.98: 7969 126.98 - 134.00: 221 Bond angle restraints: 41435 Sorted by residual: angle pdb=" C SER B 288 " pdb=" CA SER B 288 " pdb=" CB SER B 288 " ideal model delta sigma weight residual 116.34 111.55 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" N ASP C 187 " pdb=" CA ASP C 187 " pdb=" C ASP C 187 " ideal model delta sigma weight residual 113.18 109.41 3.77 1.33e+00 5.65e-01 8.04e+00 angle pdb=" N ASP A 380 " pdb=" CA ASP A 380 " pdb=" CB ASP A 380 " ideal model delta sigma weight residual 113.65 109.84 3.81 1.47e+00 4.63e-01 6.72e+00 angle pdb=" C3' U V 17 " pdb=" O3' U V 17 " pdb=" P C V 18 " ideal model delta sigma weight residual 120.20 123.61 -3.41 1.50e+00 4.44e-01 5.17e+00 angle pdb=" N CYS C 146 " pdb=" CA CYS C 146 " pdb=" C CYS C 146 " ideal model delta sigma weight residual 113.18 110.43 2.75 1.21e+00 6.83e-01 5.15e+00 ... (remaining 41430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.87: 10198 28.87 - 57.74: 565 57.74 - 86.61: 88 86.61 - 115.48: 6 115.48 - 144.35: 3 Dihedral angle restraints: 10860 sinusoidal: 6271 harmonic: 4589 Sorted by residual: dihedral pdb=" C4' U V 17 " pdb=" C3' U V 17 " pdb=" O3' U V 17 " pdb=" P C V 18 " ideal model delta sinusoidal sigma weight residual -110.00 11.04 -121.04 1 3.50e+01 8.16e-04 1.19e+01 dihedral pdb=" CA ASP B 406 " pdb=" CB ASP B 406 " pdb=" CG ASP B 406 " pdb=" OD1 ASP B 406 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" C4' A V 29 " pdb=" C3' A V 29 " pdb=" O3' A V 29 " pdb=" P G V 30 " ideal model delta sinusoidal sigma weight residual -110.00 2.88 -112.88 1 3.50e+01 8.16e-04 1.09e+01 ... (remaining 10857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1162 0.027 - 0.053: 498 0.053 - 0.080: 89 0.080 - 0.107: 59 0.107 - 0.134: 37 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA VAL C 112 " pdb=" N VAL C 112 " pdb=" C VAL C 112 " pdb=" CB VAL C 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 252 " pdb=" N VAL A 252 " pdb=" C VAL A 252 " pdb=" CB VAL A 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1842 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 162 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " -0.109 9.50e-02 1.11e+02 3.66e-02 1.66e+00 pdb=" NE ARG A 141 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 141 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 141 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 141 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 60 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 61 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.017 5.00e-02 4.00e+02 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1558 2.20 - 2.80: 45940 2.80 - 3.40: 62293 3.40 - 4.00: 84193 4.00 - 4.60: 129077 Nonbonded interactions: 323061 Sorted by model distance: nonbonded pdb=" H ASN C 299 " pdb=" OE2 GLU C 364 " model vdw 1.599 1.850 nonbonded pdb="HH12 ARG A 372 " pdb=" O GLY B 7 " model vdw 1.601 1.850 nonbonded pdb=" O LEU A 215 " pdb=" HH TYR A 403 " model vdw 1.605 1.850 nonbonded pdb=" OP2 U V 37 " pdb="HO2' U V 38 " model vdw 1.612 1.850 nonbonded pdb="HH22 ARG C 11 " pdb=" OE2 GLU C 18 " model vdw 1.643 1.850 ... (remaining 323056 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: 3.310 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: 0.320 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 88.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.003 0.042 11873 Z= 0.169 Angle : 0.457 4.786 16251 Z= 0.240 Chirality : 0.036 0.134 1845 Planarity : 0.003 0.048 1937 Dihedral : 18.088 144.349 4710 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 0.09 % Allowed : 15.71 % Favored : 84.21 % 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: 1.13 (0.24), residues: 1348 helix: 2.10 (0.24), residues: 526 sheet: -0.65 (0.42), residues: 147 loop : 0.07 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.002 0.001 HIS A 367 PHE 0.009 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.007 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8171 (ttp80) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.8789 time to fit residues: 125.0424 Evaluate side-chains 111 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11873 Z= 0.243 Angle : 0.472 4.343 16251 Z= 0.242 Chirality : 0.037 0.141 1845 Planarity : 0.003 0.042 1937 Dihedral : 14.374 143.619 2139 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 1.20 % Allowed : 14.85 % Favored : 83.95 % 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: 1.03 (0.24), residues: 1348 helix: 2.09 (0.24), residues: 528 sheet: -0.90 (0.40), residues: 149 loop : -0.01 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 299 PHE 0.011 0.001 PHE B 291 TYR 0.008 0.001 TYR A 403 ARG 0.003 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.674 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: C 59 LEU cc_start: 0.8834 (mt) cc_final: 0.8540 (mt) REVERT: C 375 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.7398 (ptp-170) outliers start: 14 outliers final: 8 residues processed: 124 average time/residue: 0.8023 time to fit residues: 127.7211 Evaluate side-chains 117 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11873 Z= 0.232 Angle : 0.462 5.181 16251 Z= 0.236 Chirality : 0.037 0.153 1845 Planarity : 0.004 0.084 1937 Dihedral : 13.924 142.760 2139 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 1.12 % Allowed : 15.28 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1348 helix: 2.08 (0.24), residues: 528 sheet: -0.92 (0.41), residues: 147 loop : -0.09 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 239 HIS 0.003 0.001 HIS B 474 PHE 0.010 0.001 PHE C 161 TYR 0.008 0.001 TYR A 403 ARG 0.007 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.661 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: B 63 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7377 (mmt90) REVERT: B 68 ASP cc_start: 0.8492 (m-30) cc_final: 0.8285 (m-30) REVERT: B 159 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 59 LEU cc_start: 0.8827 (mt) cc_final: 0.8517 (mt) REVERT: C 389 ARG cc_start: 0.8258 (mmt180) cc_final: 0.7901 (mmt180) outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 0.8186 time to fit residues: 131.3445 Evaluate side-chains 118 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11873 Z= 0.259 Angle : 0.471 4.700 16251 Z= 0.242 Chirality : 0.037 0.146 1845 Planarity : 0.004 0.067 1937 Dihedral : 13.941 141.558 2139 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 1.46 % Allowed : 15.28 % Favored : 83.26 % 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: 0.88 (0.24), residues: 1348 helix: 2.01 (0.24), residues: 528 sheet: -0.98 (0.40), residues: 147 loop : -0.15 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 299 PHE 0.010 0.001 PHE C 161 TYR 0.008 0.001 TYR A 403 ARG 0.008 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.805 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: B 63 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7399 (mmt90) REVERT: B 159 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8533 (mt) REVERT: C 59 LEU cc_start: 0.8845 (mt) cc_final: 0.8522 (mt) REVERT: C 389 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7821 (mmt180) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.8385 time to fit residues: 135.3740 Evaluate side-chains 123 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11873 Z= 0.265 Angle : 0.473 4.789 16251 Z= 0.243 Chirality : 0.037 0.144 1845 Planarity : 0.004 0.076 1937 Dihedral : 13.946 140.476 2139 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.93 % Favored : 95.92 % Rotamer: Outliers : 1.72 % Allowed : 15.36 % Favored : 82.92 % 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: 0.81 (0.24), residues: 1348 helix: 1.95 (0.24), residues: 530 sheet: -1.00 (0.40), residues: 147 loop : -0.20 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 239 HIS 0.003 0.001 HIS A 299 PHE 0.010 0.001 PHE C 161 TYR 0.008 0.001 TYR A 403 ARG 0.010 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.680 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: B 63 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7411 (mmt90) REVERT: B 159 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8551 (mt) REVERT: C 59 LEU cc_start: 0.8839 (mt) cc_final: 0.8512 (mt) REVERT: C 375 ARG cc_start: 0.7608 (ptp-170) cc_final: 0.7389 (ptp-170) REVERT: C 389 ARG cc_start: 0.8209 (mmt180) cc_final: 0.7785 (mmt180) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.7989 time to fit residues: 129.7008 Evaluate side-chains 121 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11873 Z= 0.266 Angle : 0.474 4.747 16251 Z= 0.244 Chirality : 0.037 0.144 1845 Planarity : 0.004 0.073 1937 Dihedral : 13.957 139.050 2139 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 1.63 % Allowed : 15.54 % Favored : 82.83 % 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: 0.74 (0.24), residues: 1348 helix: 1.91 (0.24), residues: 530 sheet: -1.06 (0.40), residues: 147 loop : -0.24 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 239 HIS 0.003 0.001 HIS A 299 PHE 0.011 0.001 PHE C 161 TYR 0.008 0.001 TYR A 403 ARG 0.011 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.811 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: B 63 ARG cc_start: 0.7610 (mtt-85) cc_final: 0.7407 (mmt90) REVERT: B 159 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8592 (mt) REVERT: C 59 LEU cc_start: 0.8834 (mt) cc_final: 0.8526 (mt) REVERT: C 111 ARG cc_start: 0.7457 (ptp90) cc_final: 0.7145 (ptt-90) REVERT: C 375 ARG cc_start: 0.7595 (ptp-170) cc_final: 0.7388 (ptp-170) outliers start: 19 outliers final: 16 residues processed: 122 average time/residue: 0.8223 time to fit residues: 129.3690 Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11873 Z= 0.224 Angle : 0.461 4.981 16251 Z= 0.237 Chirality : 0.036 0.142 1845 Planarity : 0.004 0.069 1937 Dihedral : 13.917 138.182 2139 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 1.55 % Allowed : 15.62 % Favored : 82.83 % 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: 0.81 (0.24), residues: 1348 helix: 1.98 (0.24), residues: 530 sheet: -1.05 (0.40), residues: 147 loop : -0.21 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 299 PHE 0.010 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.010 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.860 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: B 63 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7397 (mmt90) REVERT: B 159 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 59 LEU cc_start: 0.8837 (mt) cc_final: 0.8527 (mt) REVERT: C 375 ARG cc_start: 0.7580 (ptp-170) cc_final: 0.7379 (ptp-170) outliers start: 18 outliers final: 15 residues processed: 119 average time/residue: 0.8646 time to fit residues: 132.3363 Evaluate side-chains 124 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11873 Z= 0.188 Angle : 0.454 4.918 16251 Z= 0.233 Chirality : 0.036 0.140 1845 Planarity : 0.004 0.073 1937 Dihedral : 13.886 137.656 2139 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 1.55 % Allowed : 15.71 % Favored : 82.75 % 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: 0.87 (0.24), residues: 1348 helix: 2.04 (0.24), residues: 531 sheet: -1.09 (0.40), residues: 149 loop : -0.16 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.002 0.001 HIS B 378 PHE 0.009 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.010 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 59 LEU cc_start: 0.8832 (mt) cc_final: 0.8522 (mt) REVERT: C 375 ARG cc_start: 0.7588 (ptp-170) cc_final: 0.7385 (ptp-170) outliers start: 18 outliers final: 17 residues processed: 125 average time/residue: 0.8313 time to fit residues: 134.7836 Evaluate side-chains 123 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11873 Z= 0.161 Angle : 0.441 4.778 16251 Z= 0.226 Chirality : 0.036 0.139 1845 Planarity : 0.004 0.080 1937 Dihedral : 13.821 136.840 2139 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 1.46 % Allowed : 15.71 % Favored : 82.83 % 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: 0.96 (0.24), residues: 1348 helix: 2.12 (0.24), residues: 533 sheet: -1.00 (0.40), residues: 147 loop : -0.13 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 371 PHE 0.010 0.001 PHE C 161 TYR 0.008 0.001 TYR A 403 ARG 0.011 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.752 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: B 21 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8003 (ptmm) REVERT: B 159 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 59 LEU cc_start: 0.8823 (mt) cc_final: 0.8508 (mt) REVERT: C 343 ASP cc_start: 0.8284 (t0) cc_final: 0.7968 (t0) REVERT: C 375 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.7374 (ptp-170) outliers start: 17 outliers final: 15 residues processed: 124 average time/residue: 0.8233 time to fit residues: 130.4999 Evaluate side-chains 123 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 125 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11873 Z= 0.277 Angle : 0.475 4.988 16251 Z= 0.244 Chirality : 0.037 0.143 1845 Planarity : 0.004 0.075 1937 Dihedral : 13.885 135.405 2139 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % Rotamer: Outliers : 1.63 % Allowed : 16.05 % Favored : 82.32 % 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: 0.78 (0.24), residues: 1348 helix: 1.98 (0.24), residues: 530 sheet: -1.18 (0.40), residues: 149 loop : -0.21 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 299 PHE 0.010 0.001 PHE C 44 TYR 0.008 0.001 TYR C 99 ARG 0.010 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8016 (ptmm) REVERT: B 159 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (mt) REVERT: C 59 LEU cc_start: 0.8818 (mt) cc_final: 0.8501 (mt) outliers start: 19 outliers final: 17 residues processed: 121 average time/residue: 0.8318 time to fit residues: 127.9547 Evaluate side-chains 122 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.104940 restraints weight = 43062.749| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.96 r_work: 0.3105 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 11873 Z= 0.358 Angle : 0.766 59.199 16251 Z= 0.454 Chirality : 0.037 0.324 1845 Planarity : 0.004 0.073 1937 Dihedral : 13.888 135.389 2139 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 1.55 % Allowed : 16.22 % Favored : 82.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1348 helix: 1.97 (0.24), residues: 530 sheet: -1.18 (0.40), residues: 149 loop : -0.22 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 367 PHE 0.010 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.008 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.96 seconds wall clock time: 93 minutes 3.16 seconds (5583.16 seconds total)