Starting phenix.real_space_refine on Sat May 11 19:20:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/05_2024/8v24_42897_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/05_2024/8v24_42897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/05_2024/8v24_42897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/05_2024/8v24_42897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/05_2024/8v24_42897_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v24_42897/05_2024/8v24_42897_trim_updated.pdb" } resolution = 3.6 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= 0.064 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 C 6310 2.51 5 N 1764 2.21 5 O 1901 1.98 5 H 9601 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 270": "OE1" <-> "OE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 331": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 19652 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5165 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 4, 'TRANS': 322} Chain: "B" Number of atoms: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4595 Classifications: {'peptide': 301} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "C" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 5167 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 318} Chain: "D" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4609 Classifications: {'peptide': 302} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 289} 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, '24G': 1, 'ACT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, '24G': 1, 'ACT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4669 SG CYS A 357 55.527 54.008 44.022 1.00 66.24 S ATOM 4719 SG CYS A 360 52.507 56.006 45.208 1.00 63.26 S ATOM 4897 SG CYS A 371 53.294 55.609 41.513 1.00 60.78 S ATOM 4933 SG CYS A 374 55.482 57.829 43.701 1.00 62.49 S ATOM 14412 SG CYS C 357 34.062 52.227 59.516 1.00 59.78 S ATOM 14462 SG CYS C 360 37.401 54.248 59.253 1.00 58.85 S ATOM 14640 SG CYS C 371 36.302 52.894 62.486 1.00 56.68 S ATOM 14676 SG CYS C 374 34.343 55.749 60.926 1.00 58.27 S Time building chain proxies: 8.87, per 1000 atoms: 0.45 Number of scatterers: 19652 At special positions: 0 Unit cell: (90.78, 108.936, 111.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 68 16.00 P 4 15.00 O 1901 8.00 N 1764 7.00 C 6310 6.00 H 9601 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: 14.98 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 371 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 357 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 360 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 374 " pdb=" ZN B 403 " pdb="ZN ZN B 403 " - pdb=" NE2 HIS B 238 " pdb="ZN ZN B 403 " - pdb=" NE2 HIS B 79 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 371 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 374 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 360 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 357 " pdb=" ZN D 403 " pdb="ZN ZN D 403 " - pdb=" NE2 HIS D 238 " pdb="ZN ZN D 403 " - pdb=" NE2 HIS D 79 " Number of angles added : 12 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 11 sheets defined 46.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 103 through 120 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.763A pdb=" N SER A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.818A pdb=" N ARG A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.942A pdb=" N THR A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.620A pdb=" N ALA A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.620A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 4.268A pdb=" N LYS A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 345 through 348 No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.609A pdb=" N SER B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 234 through 250 removed outlier: 3.664A pdb=" N MET B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N CYS B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 removed outlier: 3.724A pdb=" N ASN B 269 " --> pdb=" O HIS B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.592A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 120 Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.557A pdb=" N ASP C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 153 Processing helix chain 'C' and resid 157 through 169 removed outlier: 4.013A pdb=" N ASP C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 196 through 209 Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.974A pdb=" N ARG C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 removed outlier: 4.405A pdb=" N SER C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 252 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 282 through 311 removed outlier: 7.723A pdb=" N SER C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N GLU C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 351 removed outlier: 3.761A pdb=" N GLU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 87 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 179 through 185 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.674A pdb=" N MET D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N CYS D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 277 Processing sheet with id= A, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= B, first strand: chain 'B' and resid 11 through 16 Processing sheet with id= C, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.605A pdb=" N VAL B 48 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 128 through 132 Processing sheet with id= E, first strand: chain 'B' and resid 136 through 139 removed outlier: 3.752A pdb=" N ALA B 260 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 173 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 194 removed outlier: 5.780A pdb=" N ILE B 216 " --> pdb=" O GLY B 193 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 355 through 357 Processing sheet with id= H, first strand: chain 'D' and resid 5 through 7 Processing sheet with id= I, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.530A pdb=" N ILE D 38 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL D 96 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG D 40 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 129 through 132 Processing sheet with id= K, first strand: chain 'D' and resid 136 through 139 431 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 15.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9577 1.03 - 1.23: 34 1.23 - 1.42: 4243 1.42 - 1.61: 5858 1.61 - 1.81: 112 Bond restraints: 19824 Sorted by residual: bond pdb=" N MET D 1 " pdb=" H3 MET D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N MET B 1 " pdb=" H2 MET B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N MET B 1 " pdb=" H3 MET B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N MET D 1 " pdb=" H2 MET D 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ASN B 45 " pdb=" CA ASN B 45 " ideal model delta sigma weight residual 1.462 1.493 -0.032 9.50e-03 1.11e+04 1.13e+01 ... (remaining 19819 not shown) Histogram of bond angle deviations from ideal: 74.05 - 86.10: 3 86.10 - 98.16: 3 98.16 - 110.21: 18646 110.21 - 122.26: 14057 122.26 - 134.31: 2850 Bond angle restraints: 35559 Sorted by residual: angle pdb=" C ASP A 343 " pdb=" CA ASP A 343 " pdb=" HA ASP A 343 " ideal model delta sigma weight residual 109.00 74.05 34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N ASP A 343 " pdb=" CA ASP A 343 " pdb=" HA ASP A 343 " ideal model delta sigma weight residual 110.00 75.67 34.33 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB ASP A 343 " pdb=" CA ASP A 343 " pdb=" HA ASP A 343 " ideal model delta sigma weight residual 109.00 75.31 33.69 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C PRO D 46 " pdb=" CA PRO D 46 " pdb=" CB PRO D 46 " ideal model delta sigma weight residual 110.92 122.35 -11.43 1.22e+00 6.72e-01 8.77e+01 angle pdb=" N PRO D 46 " pdb=" CA PRO D 46 " pdb=" CB PRO D 46 " ideal model delta sigma weight residual 103.08 96.05 7.03 9.70e-01 1.06e+00 5.25e+01 ... (remaining 35554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 8888 33.80 - 67.61: 420 67.61 - 101.41: 54 101.41 - 135.21: 11 135.21 - 169.02: 5 Dihedral angle restraints: 9378 sinusoidal: 5164 harmonic: 4214 Sorted by residual: dihedral pdb=" CA ARG A 342 " pdb=" C ARG A 342 " pdb=" N ASP A 343 " pdb=" CA ASP A 343 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C1 24G B 401 " pdb=" C6 24G B 401 " pdb=" C7 24G B 401 " pdb=" O8 24G B 401 " ideal model delta sinusoidal sigma weight residual -175.79 -6.77 -169.02 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O5 24G B 401 " pdb=" C6 24G B 401 " pdb=" C7 24G B 401 " pdb=" O8 24G B 401 " ideal model delta sinusoidal sigma weight residual 63.21 -129.86 -166.93 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1422 0.075 - 0.149: 104 0.149 - 0.224: 5 0.224 - 0.299: 0 0.299 - 0.373: 1 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ASP A 343 " pdb=" N ASP A 343 " pdb=" C ASP A 343 " pdb=" CB ASP A 343 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA PHE D 50 " pdb=" N PHE D 50 " pdb=" C PHE D 50 " pdb=" CB PHE D 50 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 1529 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 45 " 0.067 2.00e-02 2.50e+03 4.39e-01 2.90e+03 pdb=" CG ASN D 45 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN D 45 " -0.074 2.00e-02 2.50e+03 pdb=" ND2 ASN D 45 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 45 " -0.760 2.00e-02 2.50e+03 pdb="HD22 ASN D 45 " 0.756 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 45 " -0.101 2.00e-02 2.50e+03 4.36e-01 2.85e+03 pdb=" CG ASN B 45 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN B 45 " 0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 45 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 45 " 0.746 2.00e-02 2.50e+03 pdb="HD22 ASN B 45 " -0.750 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 46 " 0.027 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C PRO D 46 " -0.090 2.00e-02 2.50e+03 pdb=" O PRO D 46 " 0.032 2.00e-02 2.50e+03 pdb=" N PRO D 47 " 0.031 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1357 2.20 - 2.80: 40189 2.80 - 3.40: 54265 3.40 - 4.00: 70775 4.00 - 4.60: 111044 Nonbonded interactions: 277630 Sorted by model distance: nonbonded pdb=" H ASP A 343 " pdb=" HA ASP A 343 " model vdw 1.599 1.816 nonbonded pdb=" HH TYR D 39 " pdb=" OD1 ASN D 81 " model vdw 1.632 1.850 nonbonded pdb=" HE ARG C 80 " pdb=" OD1 ASP C 116 " model vdw 1.632 1.850 nonbonded pdb=" H ARG B 190 " pdb=" OE2 GLU B 234 " model vdw 1.633 1.850 nonbonded pdb=" OD1 ASP D 90 " pdb=" HZ2 LYS D 127 " model vdw 1.635 1.850 ... (remaining 277625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 389 or resid 401)) selection = (chain 'C' and ((resid 67 and (name N or name CA or name C or name O )) or (resi \ d 68 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2)) or resid 69 through 346 or (resid 347 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 348 th \ rough 386 or (resid 387 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 388 and (name N or name CA or name \ C or name O )) or (resid 389 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or resid 401)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 286 or (resid 287 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 288 through 301 or resid 401 through 403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.290 Extract box with map and model: 3.120 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 69.100 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 : 0.004 0.104 10223 Z= 0.266 Angle : 0.630 11.426 13797 Z= 0.365 Chirality : 0.040 0.373 1532 Planarity : 0.004 0.099 1786 Dihedral : 20.509 169.017 3930 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Rotamer: Outliers : 0.48 % Allowed : 22.33 % Favored : 77.19 % 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: 0.06 (0.25), residues: 1245 helix: 1.43 (0.22), residues: 632 sheet: -1.62 (0.38), residues: 172 loop : -1.25 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 268 HIS 0.006 0.001 HIS B 238 PHE 0.042 0.001 PHE D 50 TYR 0.011 0.001 TYR C 230 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.7947 (mtp) cc_final: 0.7570 (mtt) outliers start: 5 outliers final: 2 residues processed: 139 average time/residue: 0.4989 time to fit residues: 97.2173 Evaluate side-chains 132 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 236 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0170 chunk 93 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10223 Z= 0.258 Angle : 0.521 9.645 13797 Z= 0.266 Chirality : 0.040 0.349 1532 Planarity : 0.005 0.144 1786 Dihedral : 14.143 170.492 1526 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.99 % Favored : 92.85 % Rotamer: Outliers : 1.91 % Allowed : 21.09 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.11 (0.25), residues: 1245 helix: 1.40 (0.22), residues: 636 sheet: -1.43 (0.39), residues: 163 loop : -1.24 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.009 0.001 HIS B 238 PHE 0.011 0.001 PHE B 50 TYR 0.009 0.001 TYR B 39 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7548 (mp) outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.4730 time to fit residues: 98.5392 Evaluate side-chains 138 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 175 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10223 Z= 0.367 Angle : 0.520 9.168 13797 Z= 0.282 Chirality : 0.040 0.359 1532 Planarity : 0.005 0.141 1786 Dihedral : 10.713 128.151 1525 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.31 % Favored : 92.53 % Rotamer: Outliers : 2.96 % Allowed : 20.32 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.06 (0.25), residues: 1245 helix: 1.27 (0.21), residues: 635 sheet: -1.37 (0.39), residues: 168 loop : -1.40 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 268 HIS 0.010 0.001 HIS B 238 PHE 0.012 0.001 PHE B 50 TYR 0.012 0.001 TYR A 368 ARG 0.002 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 112 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7938 (t) REVERT: B 292 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: C 195 ASP cc_start: 0.6455 (t0) cc_final: 0.5952 (t0) REVERT: D 9 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7626 (mtm110) outliers start: 31 outliers final: 20 residues processed: 154 average time/residue: 0.4613 time to fit residues: 102.2490 Evaluate side-chains 147 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 10223 Z= 0.144 Angle : 0.430 8.751 13797 Z= 0.229 Chirality : 0.037 0.350 1532 Planarity : 0.004 0.137 1786 Dihedral : 9.515 118.050 1525 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 1.62 % Allowed : 20.80 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.37 (0.25), residues: 1245 helix: 1.62 (0.22), residues: 634 sheet: -1.24 (0.40), residues: 162 loop : -1.15 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 268 HIS 0.005 0.001 HIS B 238 PHE 0.016 0.001 PHE A 318 TYR 0.008 0.001 TYR B 39 ARG 0.001 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7511 (mp) REVERT: A 339 MET cc_start: 0.8141 (tpt) cc_final: 0.7662 (tpt) REVERT: B 112 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (t) REVERT: C 315 MET cc_start: 0.8344 (mmp) cc_final: 0.8131 (mmt) REVERT: D 9 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7668 (mtm110) outliers start: 17 outliers final: 7 residues processed: 145 average time/residue: 0.4620 time to fit residues: 96.3396 Evaluate side-chains 133 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 9 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 10223 Z= 0.501 Angle : 0.568 9.385 13797 Z= 0.312 Chirality : 0.043 0.358 1532 Planarity : 0.005 0.139 1786 Dihedral : 8.972 101.002 1524 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.71 % Favored : 92.13 % Rotamer: Outliers : 2.86 % Allowed : 21.28 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.14 (0.25), residues: 1245 helix: 1.20 (0.21), residues: 636 sheet: -1.29 (0.40), residues: 168 loop : -1.49 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.012 0.001 HIS B 238 PHE 0.014 0.002 PHE B 50 TYR 0.016 0.002 TYR A 368 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7562 (mp) REVERT: B 112 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7861 (t) REVERT: B 295 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7618 (tt) REVERT: C 195 ASP cc_start: 0.6522 (t0) cc_final: 0.5997 (t0) REVERT: D 9 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7637 (mtm110) outliers start: 30 outliers final: 23 residues processed: 153 average time/residue: 0.4612 time to fit residues: 101.1323 Evaluate side-chains 153 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 219 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 10223 Z= 0.146 Angle : 0.433 8.722 13797 Z= 0.232 Chirality : 0.038 0.351 1532 Planarity : 0.004 0.136 1786 Dihedral : 7.561 81.668 1524 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 1.62 % Allowed : 21.85 % Favored : 76.53 % 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: 0.35 (0.25), residues: 1245 helix: 1.60 (0.22), residues: 633 sheet: -1.19 (0.41), residues: 162 loop : -1.18 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 268 HIS 0.004 0.001 HIS B 238 PHE 0.010 0.001 PHE A 318 TYR 0.009 0.001 TYR B 39 ARG 0.002 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 112 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8032 (t) REVERT: C 327 ASN cc_start: 0.7422 (m-40) cc_final: 0.7014 (m110) REVERT: D 9 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7678 (mtm110) outliers start: 17 outliers final: 11 residues processed: 143 average time/residue: 0.4722 time to fit residues: 97.1674 Evaluate side-chains 140 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 175 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10223 Z= 0.223 Angle : 0.451 8.607 13797 Z= 0.243 Chirality : 0.038 0.354 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.489 83.968 1524 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 1.53 % Allowed : 22.04 % Favored : 76.43 % 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: 0.36 (0.25), residues: 1245 helix: 1.60 (0.22), residues: 633 sheet: -1.22 (0.40), residues: 162 loop : -1.15 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.008 0.001 HIS B 238 PHE 0.025 0.001 PHE A 318 TYR 0.009 0.001 TYR A 368 ARG 0.002 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7523 (mp) REVERT: B 112 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8024 (t) REVERT: C 327 ASN cc_start: 0.7392 (m-40) cc_final: 0.7042 (m110) REVERT: D 9 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7667 (mtm110) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.5002 time to fit residues: 101.3457 Evaluate side-chains 139 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 175 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10223 Z= 0.206 Angle : 0.443 8.591 13797 Z= 0.239 Chirality : 0.038 0.354 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.446 86.711 1524 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 1.91 % Allowed : 21.95 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1245 helix: 1.65 (0.22), residues: 632 sheet: -1.21 (0.40), residues: 162 loop : -1.14 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.007 0.001 HIS B 238 PHE 0.022 0.001 PHE A 318 TYR 0.009 0.001 TYR B 39 ARG 0.002 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7522 (mp) REVERT: A 118 MET cc_start: 0.7456 (ttp) cc_final: 0.7188 (mtp) REVERT: A 339 MET cc_start: 0.8173 (tpt) cc_final: 0.7676 (tpt) REVERT: B 112 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8040 (t) REVERT: D 9 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7696 (mtm110) outliers start: 20 outliers final: 14 residues processed: 146 average time/residue: 0.4618 time to fit residues: 97.1928 Evaluate side-chains 144 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 175 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10223 Z= 0.214 Angle : 0.449 8.704 13797 Z= 0.242 Chirality : 0.038 0.358 1532 Planarity : 0.004 0.135 1786 Dihedral : 7.451 89.375 1524 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.18 % Favored : 93.65 % Rotamer: Outliers : 1.81 % Allowed : 21.95 % Favored : 76.24 % 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: 0.42 (0.25), residues: 1245 helix: 1.67 (0.22), residues: 632 sheet: -1.21 (0.40), residues: 162 loop : -1.13 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.008 0.001 HIS B 238 PHE 0.013 0.001 PHE A 318 TYR 0.009 0.001 TYR A 368 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7524 (mp) REVERT: A 97 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6600 (mm-30) REVERT: A 118 MET cc_start: 0.7464 (ttp) cc_final: 0.7191 (mtp) REVERT: A 339 MET cc_start: 0.8177 (tpt) cc_final: 0.7683 (tpt) REVERT: A 348 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7637 (ptmm) REVERT: B 112 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8039 (t) REVERT: D 9 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7771 (mtm110) REVERT: D 292 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5744 (pt0) outliers start: 19 outliers final: 13 residues processed: 145 average time/residue: 0.5031 time to fit residues: 103.4899 Evaluate side-chains 145 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 292 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 10223 Z= 0.153 Angle : 0.434 8.599 13797 Z= 0.231 Chirality : 0.038 0.368 1532 Planarity : 0.004 0.134 1786 Dihedral : 7.308 88.444 1524 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 1.53 % Allowed : 22.42 % Favored : 76.05 % 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: 0.56 (0.26), residues: 1245 helix: 1.78 (0.22), residues: 633 sheet: -1.14 (0.40), residues: 162 loop : -1.08 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 268 HIS 0.006 0.001 HIS B 238 PHE 0.011 0.001 PHE A 318 TYR 0.007 0.001 TYR B 39 ARG 0.001 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7490 (mp) REVERT: A 97 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6622 (mm-30) REVERT: A 118 MET cc_start: 0.7420 (ttp) cc_final: 0.7149 (mtp) REVERT: A 339 MET cc_start: 0.8135 (tpt) cc_final: 0.7640 (tpt) REVERT: B 97 ASN cc_start: 0.8627 (p0) cc_final: 0.8362 (p0) REVERT: B 112 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8037 (t) REVERT: D 9 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7757 (mtm110) outliers start: 16 outliers final: 13 residues processed: 143 average time/residue: 0.4982 time to fit residues: 102.2369 Evaluate side-chains 141 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 292 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.126831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.094839 restraints weight = 34623.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.099758 restraints weight = 16928.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102933 restraints weight = 10926.497| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10223 Z= 0.179 Angle : 0.437 8.605 13797 Z= 0.234 Chirality : 0.038 0.368 1532 Planarity : 0.004 0.134 1786 Dihedral : 7.309 89.735 1524 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.62 % Favored : 94.22 % Rotamer: Outliers : 1.72 % Allowed : 22.81 % Favored : 75.48 % 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 (0.26), residues: 1245 helix: 1.82 (0.22), residues: 632 sheet: -1.10 (0.40), residues: 162 loop : -1.07 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 268 HIS 0.007 0.001 HIS B 238 PHE 0.037 0.001 PHE A 318 TYR 0.008 0.001 TYR B 39 ARG 0.002 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.67 seconds wall clock time: 74 minutes 15.65 seconds (4455.65 seconds total)