Starting phenix.real_space_refine on Fri Jul 19 02:17:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/07_2024/8tgh_41236_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/07_2024/8tgh_41236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/07_2024/8tgh_41236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/07_2024/8tgh_41236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/07_2024/8tgh_41236_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgh_41236/07_2024/8tgh_41236_trim.cif" } resolution = 3.5 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3843 2.51 5 N 900 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5778 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2860 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2864 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.86 Number of scatterers: 5778 At special positions: 0 Unit cell: (77.688, 62.416, 114.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 978 8.00 N 900 7.00 C 3843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE A 601 " Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.868A pdb=" N VAL A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Proline residue: A 43 - end of helix Proline residue: A 46 - end of helix removed outlier: 3.828A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.506A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 157 through 165 removed outlier: 4.041A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 189 through 219 removed outlier: 3.766A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.524A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.793A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.715A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.162A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 3.540A pdb=" N SER A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 421 Proline residue: A 412 - end of helix removed outlier: 4.107A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 456 removed outlier: 3.622A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.941A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.524A pdb=" N TYR A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.098A pdb=" N VAL B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.768A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 165 removed outlier: 4.120A pdb=" N GLU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.407A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.540A pdb=" N GLY B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.864A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 242 removed outlier: 3.882A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.838A pdb=" N GLY B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.825A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 318 removed outlier: 3.797A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 364 removed outlier: 3.514A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.542A pdb=" N CYS B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 removed outlier: 3.617A pdb=" N ALA B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.552A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.879A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.692A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 441 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 861 1.28 - 1.41: 1471 1.41 - 1.54: 3480 1.54 - 1.68: 10 1.68 - 1.81: 100 Bond restraints: 5922 Sorted by residual: bond pdb=" C ALA B 244 " pdb=" O ALA B 244 " ideal model delta sigma weight residual 1.244 1.157 0.087 1.00e-02 1.00e+04 7.62e+01 bond pdb=" C LEU B 238 " pdb=" O LEU B 238 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.17e-02 7.31e+03 4.13e+01 bond pdb=" C PRO B 245 " pdb=" O PRO B 245 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.76e-02 3.23e+03 2.71e+01 bond pdb=" C GLY B 243 " pdb=" O GLY B 243 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.35e-02 5.49e+03 2.62e+01 bond pdb=" C VAL B 242 " pdb=" O VAL B 242 " ideal model delta sigma weight residual 1.230 1.161 0.069 1.57e-02 4.06e+03 1.92e+01 ... (remaining 5917 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.26: 208 106.26 - 113.89: 3385 113.89 - 121.53: 3399 121.53 - 129.16: 1040 129.16 - 136.80: 34 Bond angle restraints: 8066 Sorted by residual: angle pdb=" CA ALA B 244 " pdb=" C ALA B 244 " pdb=" O ALA B 244 " ideal model delta sigma weight residual 118.79 110.51 8.28 9.60e-01 1.09e+00 7.45e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 130.32 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" N GLY A 243 " pdb=" CA GLY A 243 " pdb=" C GLY A 243 " ideal model delta sigma weight residual 112.50 119.23 -6.73 1.16e+00 7.43e-01 3.36e+01 angle pdb=" C VAL B 242 " pdb=" CA VAL B 242 " pdb=" CB VAL B 242 " ideal model delta sigma weight residual 112.19 106.43 5.76 1.15e+00 7.56e-01 2.51e+01 angle pdb=" CA LEU B 241 " pdb=" C LEU B 241 " pdb=" O LEU B 241 " ideal model delta sigma weight residual 120.82 116.34 4.48 1.05e+00 9.07e-01 1.82e+01 ... (remaining 8061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 3124 23.14 - 46.28: 314 46.28 - 69.42: 28 69.42 - 92.56: 9 92.56 - 115.70: 1 Dihedral angle restraints: 3476 sinusoidal: 1320 harmonic: 2156 Sorted by residual: dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual 180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -58.04 115.70 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 3473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 877 0.078 - 0.156: 85 0.156 - 0.234: 5 0.234 - 0.312: 0 0.312 - 0.389: 2 Chirality restraints: 969 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.68 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CG LEU A 381 " pdb=" CB LEU A 381 " pdb=" CD1 LEU A 381 " pdb=" CD2 LEU A 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA VAL B 242 " pdb=" N VAL B 242 " pdb=" C VAL B 242 " pdb=" CB VAL B 242 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 966 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 42 " 0.088 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A 43 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 244 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ALA B 244 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA B 244 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO B 245 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A 473 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.047 5.00e-02 4.00e+02 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1562 2.80 - 3.32: 5507 3.32 - 3.85: 9391 3.85 - 4.37: 10124 4.37 - 4.90: 18688 Nonbonded interactions: 45272 Sorted by model distance: nonbonded pdb=" O MET A 183 " pdb=" OG SER A 187 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLU B 135 " pdb=" NH1 ARG B 138 " model vdw 2.285 2.520 nonbonded pdb=" OD1 ASP A 299 " pdb=" NH1 ARG A 421 " model vdw 2.291 2.520 nonbonded pdb=" OD2 ASP A 299 " pdb=" NE2 HIS A 422 " model vdw 2.299 2.520 nonbonded pdb=" OD1 ASN A 313 " pdb=" N 1WE A 601 " model vdw 2.309 2.520 ... (remaining 45267 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 19 through 278 or resid 289 through 482)) selection = (chain 'B' and (resid 19 through 51 or resid 136 through 482)) } 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.370 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.007 0.092 5922 Z= 0.439 Angle : 0.812 18.427 8066 Z= 0.452 Chirality : 0.049 0.389 969 Planarity : 0.010 0.131 983 Dihedral : 17.208 115.698 2106 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.98 % Allowed : 29.92 % Favored : 69.11 % 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: 0.62 (0.29), residues: 757 helix: 0.97 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.001 0.001 HIS A 167 PHE 0.033 0.002 PHE B 131 TYR 0.029 0.002 TYR B 190 ARG 0.006 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.583 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 128 average time/residue: 0.1195 time to fit residues: 22.0009 Evaluate side-chains 124 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 274 GLN B 313 ASN B 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5922 Z= 0.268 Angle : 0.645 8.900 8066 Z= 0.322 Chirality : 0.044 0.147 969 Planarity : 0.007 0.079 983 Dihedral : 6.600 74.852 874 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.25 % Allowed : 27.48 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.30), residues: 757 helix: 1.66 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS B 416 PHE 0.017 0.001 PHE B 356 TYR 0.013 0.001 TYR A 430 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.589 Fit side-chains REVERT: B 41 VAL cc_start: 0.8247 (p) cc_final: 0.8028 (t) REVERT: B 149 MET cc_start: 0.7808 (tpp) cc_final: 0.7314 (tpp) REVERT: B 168 ILE cc_start: 0.8388 (mp) cc_final: 0.8169 (mt) outliers start: 20 outliers final: 9 residues processed: 154 average time/residue: 0.1122 time to fit residues: 25.2324 Evaluate side-chains 144 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 23 optimal weight: 0.0010 chunk 55 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5922 Z= 0.214 Angle : 0.619 8.193 8066 Z= 0.303 Chirality : 0.042 0.154 969 Planarity : 0.006 0.062 983 Dihedral : 5.925 69.495 872 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.76 % Allowed : 28.29 % Favored : 68.94 % 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: 1.80 (0.31), residues: 757 helix: 1.89 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.018 0.001 PHE B 356 TYR 0.012 0.001 TYR B 471 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.619 Fit side-chains REVERT: A 200 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: B 149 MET cc_start: 0.7788 (tpp) cc_final: 0.7537 (tpp) REVERT: B 168 ILE cc_start: 0.8300 (mp) cc_final: 0.8098 (mt) REVERT: B 331 MET cc_start: 0.8517 (mtt) cc_final: 0.8311 (mtm) outliers start: 17 outliers final: 13 residues processed: 141 average time/residue: 0.1142 time to fit residues: 23.5983 Evaluate side-chains 143 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5922 Z= 0.246 Angle : 0.618 7.832 8066 Z= 0.303 Chirality : 0.042 0.151 969 Planarity : 0.006 0.054 983 Dihedral : 5.513 65.253 872 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.74 % Allowed : 27.15 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.31), residues: 757 helix: 2.00 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.44 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 416 PHE 0.022 0.001 PHE B 356 TYR 0.012 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 0.615 Fit side-chains REVERT: A 200 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: B 149 MET cc_start: 0.7778 (tpp) cc_final: 0.7484 (tpp) REVERT: B 168 ILE cc_start: 0.8280 (mp) cc_final: 0.8064 (mt) outliers start: 23 outliers final: 16 residues processed: 150 average time/residue: 0.1189 time to fit residues: 25.7194 Evaluate side-chains 151 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 0.2980 chunk 37 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5922 Z= 0.260 Angle : 0.624 7.667 8066 Z= 0.306 Chirality : 0.043 0.153 969 Planarity : 0.006 0.055 983 Dihedral : 5.276 62.302 872 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.07 % Allowed : 26.99 % Favored : 68.94 % 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: 1.94 (0.31), residues: 757 helix: 2.00 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS B 223 PHE 0.020 0.001 PHE B 356 TYR 0.014 0.001 TYR B 471 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.590 Fit side-chains REVERT: A 200 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 240 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 40 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7545 (t) REVERT: B 149 MET cc_start: 0.7788 (tpp) cc_final: 0.7538 (tpp) REVERT: B 168 ILE cc_start: 0.8277 (mp) cc_final: 0.8065 (mt) outliers start: 25 outliers final: 17 residues processed: 148 average time/residue: 0.1208 time to fit residues: 25.8719 Evaluate side-chains 148 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5922 Z= 0.245 Angle : 0.617 7.320 8066 Z= 0.304 Chirality : 0.042 0.152 969 Planarity : 0.006 0.055 983 Dihedral : 5.153 58.807 872 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.23 % Allowed : 27.64 % Favored : 68.13 % 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: 1.95 (0.31), residues: 757 helix: 2.01 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.021 0.001 PHE B 356 TYR 0.011 0.001 TYR A 476 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.847 Fit side-chains REVERT: A 177 MET cc_start: 0.7883 (ttp) cc_final: 0.7662 (ttp) REVERT: A 200 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 240 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 40 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7495 (t) REVERT: B 149 MET cc_start: 0.7762 (tpp) cc_final: 0.7478 (tpp) REVERT: B 168 ILE cc_start: 0.8263 (mp) cc_final: 0.8041 (mt) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 0.1223 time to fit residues: 26.5259 Evaluate side-chains 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5922 Z= 0.193 Angle : 0.598 6.948 8066 Z= 0.295 Chirality : 0.041 0.151 969 Planarity : 0.005 0.054 983 Dihedral : 5.030 53.971 872 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.20 % Allowed : 26.18 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.31), residues: 757 helix: 2.09 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.26 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.019 0.001 PHE B 356 TYR 0.015 0.001 TYR B 471 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.597 Fit side-chains REVERT: A 240 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 40 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7482 (t) REVERT: B 149 MET cc_start: 0.7762 (tpp) cc_final: 0.7534 (tpp) REVERT: B 168 ILE cc_start: 0.8209 (mp) cc_final: 0.8006 (mt) outliers start: 32 outliers final: 22 residues processed: 150 average time/residue: 0.1184 time to fit residues: 25.5531 Evaluate side-chains 149 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5922 Z= 0.274 Angle : 0.630 7.137 8066 Z= 0.309 Chirality : 0.043 0.158 969 Planarity : 0.006 0.055 983 Dihedral : 4.963 51.663 872 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.39 % Allowed : 26.99 % Favored : 68.62 % 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: 1.99 (0.31), residues: 757 helix: 2.02 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 167 PHE 0.019 0.002 PHE B 356 TYR 0.011 0.001 TYR A 476 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.622 Fit side-chains REVERT: A 240 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 40 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7581 (t) REVERT: B 149 MET cc_start: 0.7753 (tpp) cc_final: 0.7475 (tpp) REVERT: B 168 ILE cc_start: 0.8247 (mp) cc_final: 0.8027 (mt) REVERT: B 349 TYR cc_start: 0.8398 (t80) cc_final: 0.8087 (t80) outliers start: 27 outliers final: 21 residues processed: 149 average time/residue: 0.1128 time to fit residues: 24.6884 Evaluate side-chains 154 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.0070 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5922 Z= 0.189 Angle : 0.612 6.580 8066 Z= 0.299 Chirality : 0.041 0.155 969 Planarity : 0.005 0.054 983 Dihedral : 4.913 46.923 872 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.90 % Allowed : 27.80 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.31), residues: 757 helix: 2.12 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.020 0.001 PHE B 131 TYR 0.015 0.001 TYR B 471 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.591 Fit side-chains REVERT: A 240 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 40 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7576 (t) REVERT: B 149 MET cc_start: 0.7753 (tpp) cc_final: 0.7523 (tpp) REVERT: B 168 ILE cc_start: 0.8193 (mp) cc_final: 0.7983 (mt) REVERT: B 331 MET cc_start: 0.8472 (mtm) cc_final: 0.8202 (mtm) outliers start: 24 outliers final: 21 residues processed: 147 average time/residue: 0.1153 time to fit residues: 24.6542 Evaluate side-chains 153 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5922 Z= 0.236 Angle : 0.626 7.196 8066 Z= 0.306 Chirality : 0.042 0.169 969 Planarity : 0.005 0.054 983 Dihedral : 4.861 45.154 872 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.90 % Allowed : 27.80 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.31), residues: 757 helix: 2.09 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.40 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS B 223 PHE 0.021 0.001 PHE B 131 TYR 0.015 0.001 TYR B 166 ARG 0.002 0.000 ARG B 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.590 Fit side-chains REVERT: A 240 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 40 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7620 (t) REVERT: B 149 MET cc_start: 0.7750 (tpp) cc_final: 0.7470 (tpp) REVERT: B 168 ILE cc_start: 0.8203 (mp) cc_final: 0.7977 (mt) REVERT: B 331 MET cc_start: 0.8459 (mtm) cc_final: 0.8186 (mtm) outliers start: 24 outliers final: 22 residues processed: 146 average time/residue: 0.1162 time to fit residues: 24.5490 Evaluate side-chains 154 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.0060 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093234 restraints weight = 8173.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096176 restraints weight = 3717.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098066 restraints weight = 2051.681| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5922 Z= 0.173 Angle : 0.604 6.933 8066 Z= 0.296 Chirality : 0.041 0.165 969 Planarity : 0.006 0.053 983 Dihedral : 4.822 44.458 872 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.90 % Allowed : 27.80 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.31), residues: 757 helix: 2.20 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.35 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 336 HIS 0.001 0.000 HIS B 167 PHE 0.022 0.001 PHE B 356 TYR 0.016 0.001 TYR B 471 ARG 0.001 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.06 seconds wall clock time: 29 minutes 38.30 seconds (1778.30 seconds total)