Starting phenix.real_space_refine on Tue Mar 19 00:13:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/03_2024/8qz8_18772_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/03_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_18772/03_2024/8qz8_18772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/03_2024/8qz8_18772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/03_2024/8qz8_18772_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qz8_18772/03_2024/8qz8_18772_updated.pdb" } 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-5265/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: 11.03, per 1000 atoms: 0.49 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: 17.98 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 12 sheets defined 34.4% alpha, 10.7% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 12.08 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 4.531A pdb=" N GLN A 7 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.581A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 314 through 323 removed outlier: 4.297A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 162 through 182 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 192 through 205 removed outlier: 3.868A pdb=" N GLU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.687A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 443 through 453 Processing helix chain 'B' and resid 480 through 496 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'C' and resid 3 through 7 removed outlier: 4.394A pdb=" N SER C 7 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 34 through 53 removed outlier: 5.687A pdb=" N SER C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 422 through 425 No H-bonds generated for 'chain 'C' and resid 422 through 425' Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.084A pdb=" N VAL A 69 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU A 56 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS A 71 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 10.503A pdb=" N TRP A 198 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA A 251 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN A 200 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR A 202 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET A 255 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 241 through 243 Processing sheet with id= D, first strand: chain 'B' and resid 74 through 80 Processing sheet with id= E, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.434A pdb=" N CYS B 250 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS B 142 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU B 252 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N LEU B 144 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 209 through 211 Processing sheet with id= G, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= H, first strand: chain 'C' and resid 77 through 81 Processing sheet with id= I, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.815A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.287A pdb=" N VAL C 221 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER C 203 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS C 223 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 360 through 363 Processing sheet with id= L, first strand: chain 'C' and resid 405 through 409 removed outlier: 3.654A pdb=" N SER C 388 " --> pdb=" O MET C 415 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 417 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL C 386 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER C 419 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL C 384 " --> pdb=" O SER C 419 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 987 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: 7.82 Time building geometry restraints manager: 18.82 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: 1602 2.20 - 2.80: 46010 2.80 - 3.40: 62362 3.40 - 4.00: 84343 4.00 - 4.60: 129216 Nonbonded interactions: 323533 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 323528 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: 2.080 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: 9.270 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 87.520 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.780 ------------------------------------------------------------------------------- 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 : 1.825 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: 0.9090 time to fit residues: 130.1139 Evaluate side-chains 111 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11873 Z= 0.283 Angle : 0.476 4.609 16251 Z= 0.240 Chirality : 0.037 0.147 1845 Planarity : 0.003 0.045 1937 Dihedral : 14.252 143.353 2139 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.23 % Favored : 95.62 % Rotamer: Outliers : 1.37 % Allowed : 15.19 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1348 helix: 1.81 (0.24), residues: 533 sheet: -1.00 (0.41), residues: 151 loop : -0.04 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 44 TYR 0.009 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 131 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 128 average time/residue: 0.7973 time to fit residues: 131.4354 Evaluate side-chains 115 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 103 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: 1.9990 chunk 84 optimal weight: 0.8980 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: 0.9990 chunk 42 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** ** 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: 0.8310 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11873 Z= 0.208 Angle : 0.447 5.129 16251 Z= 0.226 Chirality : 0.036 0.143 1845 Planarity : 0.004 0.068 1937 Dihedral : 13.933 142.839 2139 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 1.20 % Allowed : 15.28 % Favored : 83.52 % 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: 0.92 (0.24), residues: 1348 helix: 1.93 (0.24), residues: 527 sheet: -0.94 (0.41), residues: 149 loop : -0.00 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 239 HIS 0.002 0.001 HIS A 299 PHE 0.009 0.001 PHE C 44 TYR 0.007 0.001 TYR A 403 ARG 0.006 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 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7348 (mmt90) REVERT: B 159 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8531 (mt) REVERT: C 216 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7324 (tptp) outliers start: 14 outliers final: 11 residues processed: 126 average time/residue: 0.8380 time to fit residues: 135.1060 Evaluate side-chains 121 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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** C 28 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11873 Z= 0.308 Angle : 0.485 5.184 16251 Z= 0.248 Chirality : 0.037 0.142 1845 Planarity : 0.004 0.069 1937 Dihedral : 14.010 141.298 2139 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 1.72 % Allowed : 15.54 % 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: 0.69 (0.24), residues: 1348 helix: 1.71 (0.24), residues: 527 sheet: -1.08 (0.40), residues: 151 loop : -0.11 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE C 44 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 135 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7400 (mmt90) REVERT: B 68 ASP cc_start: 0.8560 (m-30) cc_final: 0.8330 (m-30) REVERT: B 159 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 216 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7348 (tptp) REVERT: C 372 ASP cc_start: 0.7261 (m-30) cc_final: 0.7026 (m-30) outliers start: 20 outliers final: 16 residues processed: 130 average time/residue: 0.8433 time to fit residues: 141.3062 Evaluate side-chains 127 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 VAL 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 B residue 365 MET 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: 1.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11873 Z= 0.300 Angle : 0.480 5.267 16251 Z= 0.245 Chirality : 0.037 0.148 1845 Planarity : 0.004 0.062 1937 Dihedral : 14.002 140.133 2139 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 1.63 % Allowed : 15.79 % Favored : 82.58 % 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: 0.59 (0.24), residues: 1348 helix: 1.63 (0.24), residues: 527 sheet: -1.13 (0.40), residues: 151 loop : -0.16 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE C 161 TYR 0.008 0.001 TYR A 403 ARG 0.008 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 131 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8557 (m-30) cc_final: 0.8339 (m-30) REVERT: B 159 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8567 (mt) REVERT: C 216 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7351 (tptp) REVERT: C 372 ASP cc_start: 0.7273 (m-30) cc_final: 0.7033 (m-30) outliers start: 19 outliers final: 15 residues processed: 126 average time/residue: 0.8512 time to fit residues: 138.8918 Evaluate side-chains 127 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 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 365 MET 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: 5.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1191 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= 0.231 Angle : 0.466 4.979 16251 Z= 0.238 Chirality : 0.036 0.142 1845 Planarity : 0.004 0.058 1937 Dihedral : 13.968 139.548 2139 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 1.55 % Allowed : 16.14 % 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: 0.68 (0.24), residues: 1348 helix: 1.70 (0.24), residues: 527 sheet: -1.11 (0.40), residues: 151 loop : -0.11 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 0.008 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 135 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8560 (m-30) cc_final: 0.8339 (m-30) REVERT: B 159 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 59 LEU cc_start: 0.8916 (mt) cc_final: 0.8593 (mt) REVERT: C 372 ASP cc_start: 0.7271 (m-30) cc_final: 0.7041 (m-30) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.8008 time to fit residues: 131.6612 Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 204 GLU Chi-restraints excluded: chain B residue 365 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11873 Z= 0.172 Angle : 0.443 4.740 16251 Z= 0.225 Chirality : 0.036 0.141 1845 Planarity : 0.004 0.065 1937 Dihedral : 13.877 138.810 2139 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 1.12 % Allowed : 16.39 % Favored : 82.49 % 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: 0.84 (0.24), residues: 1348 helix: 1.86 (0.24), residues: 527 sheet: -1.06 (0.40), residues: 151 loop : -0.03 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.002 0.001 HIS A 371 PHE 0.009 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.011 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 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8561 (m-30) cc_final: 0.8356 (m-30) REVERT: B 159 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8551 (mt) REVERT: C 59 LEU cc_start: 0.8907 (mt) cc_final: 0.8580 (mt) REVERT: C 216 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7326 (tptp) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.8713 time to fit residues: 138.9147 Evaluate side-chains 121 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 SER Chi-restraints excluded: chain B residue 444 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11873 Z= 0.178 Angle : 0.439 4.621 16251 Z= 0.223 Chirality : 0.036 0.140 1845 Planarity : 0.004 0.070 1937 Dihedral : 13.828 137.745 2139 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 1.12 % Allowed : 16.91 % Favored : 81.97 % 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: 0.89 (0.24), residues: 1348 helix: 1.92 (0.24), residues: 527 sheet: -1.04 (0.40), residues: 148 loop : -0.02 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 239 HIS 0.002 0.001 HIS B 161 PHE 0.009 0.001 PHE C 161 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 126 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8560 (m-30) cc_final: 0.8344 (m-30) REVERT: B 159 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 59 LEU cc_start: 0.8904 (mt) cc_final: 0.8572 (mt) REVERT: C 216 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7326 (tptp) REVERT: C 343 ASP cc_start: 0.8239 (t0) cc_final: 0.7915 (t0) outliers start: 13 outliers final: 12 residues processed: 123 average time/residue: 0.8403 time to fit residues: 131.1636 Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 SER Chi-restraints excluded: chain B residue 444 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8314 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11873 Z= 0.184 Angle : 0.441 4.857 16251 Z= 0.224 Chirality : 0.036 0.140 1845 Planarity : 0.004 0.073 1937 Dihedral : 13.810 136.972 2139 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 1.12 % Allowed : 17.17 % Favored : 81.72 % 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: 0.89 (0.24), residues: 1348 helix: 1.93 (0.24), residues: 527 sheet: -1.04 (0.40), residues: 148 loop : -0.02 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 392 HIS 0.002 0.001 HIS A 299 PHE 0.008 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.010 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 131 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.814 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: 0.8495 (mtmm) cc_final: 0.8046 (ptmm) REVERT: B 159 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 59 LEU cc_start: 0.8898 (mt) cc_final: 0.8562 (mt) REVERT: C 343 ASP cc_start: 0.8260 (t0) cc_final: 0.7941 (t0) outliers start: 13 outliers final: 12 residues processed: 129 average time/residue: 0.8670 time to fit residues: 142.3145 Evaluate side-chains 129 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 286 SER Chi-restraints excluded: chain B residue 444 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 136 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8309 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11873 Z= 0.169 Angle : 0.438 4.800 16251 Z= 0.222 Chirality : 0.035 0.139 1845 Planarity : 0.004 0.082 1937 Dihedral : 13.775 136.029 2139 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 1.29 % Allowed : 17.00 % Favored : 81.72 % 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: 0.94 (0.24), residues: 1348 helix: 1.98 (0.24), residues: 527 sheet: -1.04 (0.40), residues: 148 loop : -0.00 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 392 HIS 0.002 0.001 HIS A 371 PHE 0.008 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.011 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 134 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8038 (ptmm) REVERT: B 159 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 111 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7166 (ptt-90) REVERT: C 216 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7324 (tptp) REVERT: C 268 ASP cc_start: 0.7651 (t0) cc_final: 0.7287 (t0) REVERT: C 343 ASP cc_start: 0.8260 (t0) cc_final: 0.7942 (t0) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.8707 time to fit residues: 143.8527 Evaluate side-chains 125 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN 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 286 SER Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 444 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106185 restraints weight = 42665.279| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.96 r_work: 0.3120 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 11873 Z= 0.278 Angle : 0.755 59.193 16251 Z= 0.447 Chirality : 0.038 0.509 1845 Planarity : 0.004 0.080 1937 Dihedral : 13.782 136.030 2139 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 1.20 % Allowed : 17.00 % Favored : 81.80 % 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: 0.93 (0.24), residues: 1348 helix: 1.97 (0.24), residues: 527 sheet: -0.99 (0.40), residues: 146 loop : -0.02 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 392 HIS 0.002 0.001 HIS A 299 PHE 0.008 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.009 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.49 seconds wall clock time: 96 minutes 46.73 seconds (5806.73 seconds total)