Starting phenix.real_space_refine on Fri Aug 2 23:54:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/08_2024/8s86_19798.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/08_2024/8s86_19798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/08_2024/8s86_19798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/08_2024/8s86_19798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/08_2024/8s86_19798.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/08_2024/8s86_19798.cif" } resolution = 2.8 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= -0.003 sd= 0.093 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 30 5.16 5 C 3919 2.51 5 N 1080 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6177 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3085 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 4 Chain: "B" Number of atoms: 3092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3092 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 23, 'TRANS': 369} Chain breaks: 7 Time building chain proxies: 3.77, per 1000 atoms: 0.61 Number of scatterers: 6177 At special positions: 0 Unit cell: (71.06, 122.265, 72.105, 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 30 16.00 O 1148 8.00 N 1080 7.00 C 3919 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: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1478 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 40.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.703A pdb=" N ALA A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.736A pdb=" N ASP A 243 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.575A pdb=" N GLY A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 4.235A pdb=" N ALA A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.655A pdb=" N SER A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 158 removed outlier: 3.670A pdb=" N ALA B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 237 through 255 removed outlier: 3.798A pdb=" N ASP B 243 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 307 through 318 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 373 through 383 removed outlier: 3.931A pdb=" N PHE B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.670A pdb=" N SER B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.734A pdb=" N GLY B 484 " --> pdb=" O ASP B 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 88 removed outlier: 3.511A pdb=" N PHE A 212 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 120 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA A 164 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 122 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N SER A 166 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER A 124 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 161 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG A 188 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 163 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 190 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 165 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 281 removed outlier: 4.685A pdb=" N THR A 305 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281 removed outlier: 4.626A pdb=" N LYS A 418 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 322 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 363 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 324 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER A 365 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL A 326 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 360 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS A 396 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 362 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE A 398 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 364 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 88 removed outlier: 3.628A pdb=" N PHE B 212 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 203 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG B 162 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 164 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 166 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 163 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 190 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 165 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 281 removed outlier: 4.618A pdb=" N THR B 305 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 281 removed outlier: 4.589A pdb=" N LYS B 418 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 322 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 363 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 324 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N SER B 365 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 326 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 360 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 396 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 362 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE B 398 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 364 " --> pdb=" O PHE B 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 330 270 hydrogen bonds defined for protein. 717 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: 1.78 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1527 1.33 - 1.45: 1294 1.45 - 1.57: 3459 1.57 - 1.69: 1 1.69 - 1.81: 46 Bond restraints: 6327 Sorted by residual: bond pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.00e-02 1.00e+04 1.14e+01 bond pdb=" CZ ARG B 350 " pdb=" NH2 ARG B 350 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.46e+00 bond pdb=" N VAL B 227 " pdb=" CA VAL B 227 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.27e+00 bond pdb=" CZ ARG A 350 " pdb=" NH2 ARG A 350 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.455 1.491 -0.037 1.27e-02 6.20e+03 8.34e+00 ... (remaining 6322 not shown) Histogram of bond angle deviations from ideal: 95.89 - 103.57: 103 103.57 - 111.26: 2447 111.26 - 118.94: 2620 118.94 - 126.63: 3313 126.63 - 134.31: 135 Bond angle restraints: 8618 Sorted by residual: angle pdb=" C PRO B 296 " pdb=" N PRO B 297 " pdb=" CA PRO B 297 " ideal model delta sigma weight residual 120.38 126.73 -6.35 1.03e+00 9.43e-01 3.80e+01 angle pdb=" CA ASP B 307 " pdb=" CB ASP B 307 " pdb=" CG ASP B 307 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP A 316 " pdb=" CB ASP A 316 " pdb=" CG ASP A 316 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.00e+00 1.00e+00 3.03e+01 angle pdb=" CB HIS B 416 " pdb=" CG HIS B 416 " pdb=" CD2 HIS B 416 " ideal model delta sigma weight residual 131.20 124.45 6.75 1.30e+00 5.92e-01 2.69e+01 angle pdb=" CA TYR B 323 " pdb=" C TYR B 323 " pdb=" N VAL B 324 " ideal model delta sigma weight residual 116.37 122.05 -5.68 1.19e+00 7.06e-01 2.28e+01 ... (remaining 8613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 3395 16.93 - 33.86: 275 33.86 - 50.78: 64 50.78 - 67.71: 7 67.71 - 84.64: 4 Dihedral angle restraints: 3745 sinusoidal: 1465 harmonic: 2280 Sorted by residual: dihedral pdb=" CA HIS B 337 " pdb=" C HIS B 337 " pdb=" N PRO B 338 " pdb=" CA PRO B 338 " ideal model delta harmonic sigma weight residual 180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA SER B 99 " pdb=" C SER B 99 " pdb=" N THR B 100 " pdb=" CA THR B 100 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ALA A 486 " pdb=" C ALA A 486 " pdb=" N CYS A 487 " pdb=" CA CYS A 487 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 782 0.084 - 0.167: 166 0.167 - 0.251: 12 0.251 - 0.335: 2 0.335 - 0.418: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ALA B 295 " pdb=" N ALA B 295 " pdb=" C ALA B 295 " pdb=" CB ALA B 295 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA ASP A 316 " pdb=" N ASP A 316 " pdb=" C ASP A 316 " pdb=" CB ASP A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA TRP A 433 " pdb=" N TRP A 433 " pdb=" C TRP A 433 " pdb=" CB TRP A 433 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 961 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 433 " -0.092 2.00e-02 2.50e+03 6.66e-02 1.11e+02 pdb=" CG TRP A 433 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP A 433 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 433 " 0.087 2.00e-02 2.50e+03 pdb=" NE1 TRP A 433 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP A 433 " 0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP A 433 " 0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 433 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 433 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 433 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 342 " 0.102 2.00e-02 2.50e+03 5.77e-02 8.32e+01 pdb=" CG TRP B 342 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP B 342 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 342 " -0.068 2.00e-02 2.50e+03 pdb=" NE1 TRP B 342 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP B 342 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP B 342 " -0.079 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 342 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 342 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 342 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 433 " -0.038 2.00e-02 2.50e+03 5.43e-02 7.38e+01 pdb=" CG TRP B 433 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP B 433 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP B 433 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP B 433 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP B 433 " 0.058 2.00e-02 2.50e+03 pdb=" CE3 TRP B 433 " 0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 433 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 433 " -0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP B 433 " -0.078 2.00e-02 2.50e+03 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1582 2.81 - 3.34: 6174 3.34 - 3.86: 10904 3.86 - 4.38: 13688 4.38 - 4.90: 21974 Nonbonded interactions: 54322 Sorted by model distance: nonbonded pdb=" OE2 GLU A 87 " pdb=" NH2 ARG A 466 " model vdw 2.292 3.120 nonbonded pdb=" NH1 ARG B 466 " pdb=" OD1 ASP B 467 " model vdw 2.301 3.120 nonbonded pdb=" NE1 TRP B 265 " pdb=" O PRO B 298 " model vdw 2.338 3.120 nonbonded pdb=" N ASP B 191 " pdb=" OD1 ASP B 191 " model vdw 2.372 3.120 nonbonded pdb=" NH1 ARG A 466 " pdb=" OD1 ASP A 467 " model vdw 2.373 3.120 ... (remaining 54317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 79 through 386 or resid 388 through 389 or resid 391 throu \ gh 490)) selection = (chain 'B' and (resid 79 through 256 or resid 265 through 334 or resid 338 throu \ gh 490)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.360 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.008 0.055 6327 Z= 0.497 Angle : 1.182 8.309 8618 Z= 0.770 Chirality : 0.068 0.418 964 Planarity : 0.013 0.142 1107 Dihedral : 13.436 84.640 2267 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.24 % Allowed : 8.37 % Favored : 89.39 % Cbeta Deviations : 0.27 % 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: -2.43 (0.26), residues: 759 helix: -2.00 (0.23), residues: 266 sheet: -0.09 (0.35), residues: 203 loop : -2.22 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.013 TRP A 433 HIS 0.018 0.002 HIS A 416 PHE 0.042 0.005 PHE B 377 TYR 0.103 0.010 TYR B 329 ARG 0.028 0.003 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.6510 (tttp) cc_final: 0.6169 (pttp) REVERT: A 234 MET cc_start: 0.7164 (ttm) cc_final: 0.6910 (tpp) REVERT: A 276 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5404 (mt-10) REVERT: B 94 ASP cc_start: 0.4739 (p0) cc_final: 0.4536 (p0) REVERT: B 107 GLN cc_start: 0.7357 (mt0) cc_final: 0.7094 (mt0) REVERT: B 276 GLU cc_start: 0.5716 (mm-30) cc_final: 0.5192 (pt0) REVERT: B 340 ARG cc_start: 0.6052 (mmm-85) cc_final: 0.5406 (tpp80) outliers start: 15 outliers final: 1 residues processed: 147 average time/residue: 1.0574 time to fit residues: 163.7442 Evaluate side-chains 93 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 201 HIS A 284 ASN A 485 ASN B 117 HIS B 197 HIS B 201 HIS B 218 ASN ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6327 Z= 0.255 Angle : 0.701 9.155 8618 Z= 0.363 Chirality : 0.047 0.174 964 Planarity : 0.005 0.045 1107 Dihedral : 5.379 18.949 850 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.14 % Allowed : 15.55 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.29), residues: 759 helix: -0.44 (0.29), residues: 271 sheet: 0.27 (0.36), residues: 201 loop : -1.30 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 205 HIS 0.007 0.001 HIS A 416 PHE 0.019 0.003 PHE B 204 TYR 0.023 0.002 TYR B 291 ARG 0.003 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3317 (OUTLIER) cc_final: 0.3017 (p) REVERT: A 167 LYS cc_start: 0.6331 (tttp) cc_final: 0.5882 (pttp) REVERT: A 234 MET cc_start: 0.7200 (ttm) cc_final: 0.6936 (tpp) REVERT: A 294 SER cc_start: 0.4425 (p) cc_final: 0.4219 (m) REVERT: B 94 ASP cc_start: 0.4609 (p0) cc_final: 0.4397 (p0) REVERT: B 282 CYS cc_start: 0.6175 (t) cc_final: 0.5958 (m) REVERT: B 327 MET cc_start: 0.6054 (ttt) cc_final: 0.5694 (tpp) REVERT: B 346 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.6009 (m-30) outliers start: 21 outliers final: 3 residues processed: 118 average time/residue: 0.9437 time to fit residues: 117.7433 Evaluate side-chains 91 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6327 Z= 0.274 Angle : 0.675 8.868 8618 Z= 0.350 Chirality : 0.046 0.154 964 Planarity : 0.005 0.044 1107 Dihedral : 5.066 21.418 848 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.53 % Allowed : 14.50 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.29), residues: 759 helix: -0.20 (0.30), residues: 271 sheet: 0.27 (0.36), residues: 199 loop : -1.26 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 205 HIS 0.009 0.001 HIS A 416 PHE 0.025 0.003 PHE B 212 TYR 0.025 0.003 TYR B 273 ARG 0.010 0.001 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3375 (OUTLIER) cc_final: 0.3124 (p) REVERT: A 180 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.4939 (mp) REVERT: A 234 MET cc_start: 0.7332 (ttm) cc_final: 0.7076 (tpp) REVERT: A 242 ARG cc_start: 0.6268 (ttm110) cc_final: 0.5798 (ttm110) REVERT: A 276 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.5108 (pt0) REVERT: A 277 THR cc_start: 0.6763 (p) cc_final: 0.6552 (p) REVERT: A 294 SER cc_start: 0.4409 (p) cc_final: 0.4208 (m) REVERT: B 94 ASP cc_start: 0.4767 (p0) cc_final: 0.4556 (p0) REVERT: B 104 SER cc_start: 0.5362 (m) cc_final: 0.4795 (p) REVERT: B 272 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6271 (pmm-80) REVERT: B 277 THR cc_start: 0.6920 (p) cc_final: 0.6718 (p) REVERT: B 340 ARG cc_start: 0.6278 (mmm160) cc_final: 0.5542 (tpt170) REVERT: B 346 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6087 (m-30) REVERT: B 371 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5606 (pm20) outliers start: 37 outliers final: 12 residues processed: 123 average time/residue: 0.8624 time to fit residues: 112.9013 Evaluate side-chains 100 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN B 117 HIS B 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6327 Z= 0.218 Angle : 0.615 7.217 8618 Z= 0.321 Chirality : 0.045 0.161 964 Planarity : 0.005 0.043 1107 Dihedral : 4.742 17.768 848 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.78 % Allowed : 15.84 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.30), residues: 759 helix: 0.01 (0.30), residues: 277 sheet: 0.31 (0.37), residues: 200 loop : -1.00 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 205 HIS 0.007 0.001 HIS A 416 PHE 0.024 0.003 PHE A 398 TYR 0.034 0.002 TYR A 291 ARG 0.004 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 0.599 Fit side-chains REVERT: A 100 THR cc_start: 0.3448 (OUTLIER) cc_final: 0.3127 (p) REVERT: A 180 LEU cc_start: 0.5466 (OUTLIER) cc_final: 0.5074 (mp) REVERT: A 234 MET cc_start: 0.7241 (ttm) cc_final: 0.6985 (tpp) REVERT: A 276 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5217 (pt0) REVERT: A 277 THR cc_start: 0.6836 (p) cc_final: 0.6616 (p) REVERT: A 346 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6114 (m-30) REVERT: B 94 ASP cc_start: 0.4761 (p0) cc_final: 0.4545 (p0) REVERT: B 104 SER cc_start: 0.5396 (m) cc_final: 0.4856 (p) REVERT: B 180 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5009 (mp) REVERT: B 272 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6386 (pmm-80) REVERT: B 305 THR cc_start: 0.6919 (OUTLIER) cc_final: 0.6704 (m) REVERT: B 340 ARG cc_start: 0.6097 (mmm160) cc_final: 0.5839 (mmm160) REVERT: B 346 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: B 371 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5588 (mp0) REVERT: B 408 ARG cc_start: 0.6608 (mtt90) cc_final: 0.6406 (mtt-85) REVERT: B 420 MET cc_start: 0.6414 (ttp) cc_final: 0.6168 (ttm) outliers start: 32 outliers final: 9 residues processed: 109 average time/residue: 0.9868 time to fit residues: 114.0212 Evaluate side-chains 90 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.0170 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6327 Z= 0.233 Angle : 0.635 9.185 8618 Z= 0.327 Chirality : 0.045 0.173 964 Planarity : 0.005 0.041 1107 Dihedral : 4.721 18.416 848 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.93 % Allowed : 18.09 % Favored : 76.98 % 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: -0.49 (0.30), residues: 759 helix: -0.02 (0.30), residues: 277 sheet: 0.36 (0.37), residues: 199 loop : -1.00 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 205 HIS 0.005 0.001 HIS A 416 PHE 0.027 0.003 PHE A 398 TYR 0.029 0.003 TYR A 291 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.3453 (OUTLIER) cc_final: 0.3136 (p) REVERT: A 160 ASN cc_start: 0.6733 (t0) cc_final: 0.5792 (m-40) REVERT: A 180 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5143 (mp) REVERT: A 234 MET cc_start: 0.7286 (ttm) cc_final: 0.7038 (tpp) REVERT: A 276 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5376 (pt0) REVERT: A 277 THR cc_start: 0.6750 (p) cc_final: 0.6534 (p) REVERT: A 346 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6093 (m-30) REVERT: B 94 ASP cc_start: 0.4768 (p0) cc_final: 0.4549 (p0) REVERT: B 104 SER cc_start: 0.5440 (m) cc_final: 0.4917 (p) REVERT: B 180 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.4811 (mp) REVERT: B 197 HIS cc_start: 0.5855 (m-70) cc_final: 0.5544 (m-70) REVERT: B 272 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6407 (pmm-80) REVERT: B 305 THR cc_start: 0.6903 (OUTLIER) cc_final: 0.6645 (m) REVERT: B 346 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: B 420 MET cc_start: 0.6223 (ttp) cc_final: 0.5952 (ttm) outliers start: 33 outliers final: 11 residues processed: 105 average time/residue: 0.8755 time to fit residues: 98.4418 Evaluate side-chains 96 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6327 Z= 0.229 Angle : 0.636 8.203 8618 Z= 0.325 Chirality : 0.045 0.155 964 Planarity : 0.005 0.041 1107 Dihedral : 4.658 17.093 848 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.78 % Allowed : 18.83 % Favored : 76.38 % 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: -0.29 (0.30), residues: 759 helix: 0.18 (0.31), residues: 269 sheet: 0.26 (0.37), residues: 201 loop : -0.72 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 205 HIS 0.005 0.001 HIS A 416 PHE 0.028 0.003 PHE B 398 TYR 0.027 0.002 TYR B 291 ARG 0.011 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 0.602 Fit side-chains REVERT: A 100 THR cc_start: 0.3373 (OUTLIER) cc_final: 0.3137 (p) REVERT: A 136 THR cc_start: 0.6422 (p) cc_final: 0.6046 (t) REVERT: A 180 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.4992 (mp) REVERT: A 234 MET cc_start: 0.7349 (ttm) cc_final: 0.7026 (tpp) REVERT: A 276 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5690 (pt0) REVERT: A 277 THR cc_start: 0.6814 (p) cc_final: 0.6567 (p) REVERT: A 346 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6188 (m-30) REVERT: B 94 ASP cc_start: 0.4826 (p0) cc_final: 0.4594 (p0) REVERT: B 104 SER cc_start: 0.5539 (m) cc_final: 0.5101 (p) REVERT: B 180 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.4798 (mp) REVERT: B 197 HIS cc_start: 0.6097 (m-70) cc_final: 0.5829 (m90) REVERT: B 273 TYR cc_start: 0.6942 (m-10) cc_final: 0.6702 (m-10) REVERT: B 305 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6627 (m) REVERT: B 340 ARG cc_start: 0.6014 (mmm160) cc_final: 0.5685 (mmm160) REVERT: B 346 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.5960 (m-30) REVERT: B 420 MET cc_start: 0.6307 (ttp) cc_final: 0.6103 (ttm) outliers start: 32 outliers final: 12 residues processed: 103 average time/residue: 0.8018 time to fit residues: 88.8633 Evaluate side-chains 92 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6327 Z= 0.230 Angle : 0.651 13.184 8618 Z= 0.330 Chirality : 0.046 0.240 964 Planarity : 0.005 0.041 1107 Dihedral : 4.601 17.072 848 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.29 % Allowed : 21.08 % Favored : 75.64 % 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: -0.29 (0.30), residues: 759 helix: 0.17 (0.31), residues: 269 sheet: 0.27 (0.37), residues: 201 loop : -0.71 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 205 HIS 0.005 0.001 HIS A 416 PHE 0.024 0.003 PHE B 398 TYR 0.028 0.002 TYR B 291 ARG 0.008 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 0.607 Fit side-chains REVERT: A 100 THR cc_start: 0.3313 (OUTLIER) cc_final: 0.3086 (p) REVERT: A 136 THR cc_start: 0.6448 (p) cc_final: 0.6066 (t) REVERT: A 160 ASN cc_start: 0.6742 (t0) cc_final: 0.5683 (m-40) REVERT: A 180 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.4929 (mp) REVERT: A 234 MET cc_start: 0.7341 (ttm) cc_final: 0.7030 (tpp) REVERT: A 276 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5899 (pt0) REVERT: A 277 THR cc_start: 0.6859 (p) cc_final: 0.6587 (p) REVERT: A 346 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6164 (m-30) REVERT: B 94 ASP cc_start: 0.4852 (p0) cc_final: 0.4624 (p0) REVERT: B 104 SER cc_start: 0.5542 (m) cc_final: 0.5116 (p) REVERT: B 180 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4796 (mp) REVERT: B 197 HIS cc_start: 0.6187 (m-70) cc_final: 0.5924 (m90) REVERT: B 305 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6591 (m) REVERT: B 340 ARG cc_start: 0.5989 (mmm160) cc_final: 0.5674 (mmm160) REVERT: B 346 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.5962 (m-30) REVERT: B 408 ARG cc_start: 0.6665 (mtt90) cc_final: 0.6413 (mtt-85) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 0.7934 time to fit residues: 78.5575 Evaluate side-chains 88 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6327 Z= 0.238 Angle : 0.658 13.033 8618 Z= 0.332 Chirality : 0.046 0.189 964 Planarity : 0.005 0.040 1107 Dihedral : 4.614 18.209 848 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.19 % Allowed : 20.18 % Favored : 75.64 % 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: -0.23 (0.30), residues: 759 helix: 0.24 (0.31), residues: 266 sheet: 0.35 (0.36), residues: 204 loop : -0.75 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 468 HIS 0.005 0.001 HIS A 416 PHE 0.018 0.002 PHE A 398 TYR 0.028 0.002 TYR B 291 ARG 0.007 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 0.683 Fit side-chains REVERT: A 100 THR cc_start: 0.3142 (OUTLIER) cc_final: 0.2880 (p) REVERT: A 136 THR cc_start: 0.6442 (p) cc_final: 0.6070 (t) REVERT: A 160 ASN cc_start: 0.6707 (t0) cc_final: 0.5706 (m-40) REVERT: A 180 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4799 (mp) REVERT: A 189 MET cc_start: 0.6677 (mmt) cc_final: 0.6450 (mmt) REVERT: A 234 MET cc_start: 0.7310 (ttm) cc_final: 0.7003 (tpp) REVERT: A 246 LYS cc_start: 0.4656 (ttpt) cc_final: 0.4223 (tmmt) REVERT: A 276 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5905 (pt0) REVERT: A 277 THR cc_start: 0.6854 (p) cc_final: 0.6582 (p) REVERT: A 346 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6161 (m-30) REVERT: A 374 MET cc_start: 0.6271 (ptm) cc_final: 0.5963 (ptp) REVERT: B 94 ASP cc_start: 0.4902 (p0) cc_final: 0.4676 (p0) REVERT: B 104 SER cc_start: 0.5471 (m) cc_final: 0.5106 (p) REVERT: B 180 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.4960 (mp) REVERT: B 197 HIS cc_start: 0.6198 (m-70) cc_final: 0.5877 (m90) REVERT: B 279 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6275 (ttm) REVERT: B 305 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6584 (m) REVERT: B 327 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.5390 (tpp) REVERT: B 340 ARG cc_start: 0.5974 (mmm160) cc_final: 0.5694 (mmm160) REVERT: B 346 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.5977 (m-30) REVERT: B 408 ARG cc_start: 0.6675 (mtt90) cc_final: 0.6423 (mtt-85) outliers start: 28 outliers final: 12 residues processed: 92 average time/residue: 0.8859 time to fit residues: 87.1698 Evaluate side-chains 92 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6327 Z= 0.207 Angle : 0.632 12.276 8618 Z= 0.320 Chirality : 0.045 0.161 964 Planarity : 0.004 0.040 1107 Dihedral : 4.463 18.618 848 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.99 % Allowed : 21.52 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 759 helix: 0.22 (0.32), residues: 271 sheet: 0.36 (0.36), residues: 204 loop : -0.91 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 468 HIS 0.004 0.001 HIS A 416 PHE 0.023 0.002 PHE B 268 TYR 0.039 0.002 TYR B 273 ARG 0.006 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.657 Fit side-chains REVERT: A 100 THR cc_start: 0.3153 (OUTLIER) cc_final: 0.2907 (p) REVERT: A 136 THR cc_start: 0.6419 (p) cc_final: 0.6054 (t) REVERT: A 160 ASN cc_start: 0.6708 (t0) cc_final: 0.5792 (m-40) REVERT: A 180 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.4903 (mp) REVERT: A 189 MET cc_start: 0.6739 (mmt) cc_final: 0.6497 (mmt) REVERT: A 208 ASP cc_start: 0.7377 (m-30) cc_final: 0.7023 (m-30) REVERT: A 234 MET cc_start: 0.7264 (ttm) cc_final: 0.6975 (tpp) REVERT: A 276 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5857 (pt0) REVERT: A 277 THR cc_start: 0.6869 (p) cc_final: 0.6604 (p) REVERT: A 346 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6121 (m-30) REVERT: A 374 MET cc_start: 0.6295 (ptm) cc_final: 0.5939 (ptp) REVERT: B 94 ASP cc_start: 0.4846 (p0) cc_final: 0.4613 (p0) REVERT: B 104 SER cc_start: 0.5466 (m) cc_final: 0.5149 (p) REVERT: B 180 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4913 (mp) REVERT: B 197 HIS cc_start: 0.6110 (m-70) cc_final: 0.5845 (m90) REVERT: B 305 THR cc_start: 0.6704 (OUTLIER) cc_final: 0.6473 (m) REVERT: B 340 ARG cc_start: 0.6020 (mmm160) cc_final: 0.5700 (mmm160) REVERT: B 346 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.5998 (m-30) REVERT: B 408 ARG cc_start: 0.6636 (mtt90) cc_final: 0.6409 (mtt-85) outliers start: 20 outliers final: 11 residues processed: 90 average time/residue: 0.8372 time to fit residues: 80.7900 Evaluate side-chains 86 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.0870 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6327 Z= 0.235 Angle : 0.652 12.753 8618 Z= 0.331 Chirality : 0.046 0.174 964 Planarity : 0.005 0.040 1107 Dihedral : 4.522 17.878 848 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.84 % Allowed : 22.27 % Favored : 74.89 % 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: -0.37 (0.31), residues: 759 helix: 0.20 (0.31), residues: 271 sheet: 0.28 (0.36), residues: 204 loop : -0.94 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 468 HIS 0.004 0.001 HIS A 416 PHE 0.020 0.002 PHE B 268 TYR 0.028 0.002 TYR B 291 ARG 0.006 0.000 ARG B 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.651 Fit side-chains REVERT: A 100 THR cc_start: 0.3280 (OUTLIER) cc_final: 0.2994 (p) REVERT: A 136 THR cc_start: 0.6450 (p) cc_final: 0.6083 (t) REVERT: A 160 ASN cc_start: 0.6757 (t0) cc_final: 0.5842 (m-40) REVERT: A 180 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4842 (mp) REVERT: A 234 MET cc_start: 0.7293 (ttm) cc_final: 0.6998 (tpp) REVERT: A 246 LYS cc_start: 0.4683 (ttpt) cc_final: 0.4226 (tmmt) REVERT: A 272 ARG cc_start: 0.6387 (mpp80) cc_final: 0.6030 (tpt90) REVERT: A 276 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5941 (pt0) REVERT: A 277 THR cc_start: 0.6897 (p) cc_final: 0.6633 (p) REVERT: A 374 MET cc_start: 0.6321 (ptm) cc_final: 0.5930 (ptp) REVERT: A 476 LEU cc_start: 0.6890 (tp) cc_final: 0.6508 (mt) REVERT: B 94 ASP cc_start: 0.4880 (p0) cc_final: 0.4637 (p0) REVERT: B 104 SER cc_start: 0.5626 (m) cc_final: 0.5200 (p) REVERT: B 180 LEU cc_start: 0.5508 (OUTLIER) cc_final: 0.4962 (mp) REVERT: B 197 HIS cc_start: 0.6116 (m-70) cc_final: 0.5848 (m90) REVERT: B 272 ARG cc_start: 0.7004 (pmt100) cc_final: 0.6609 (pmt-80) REVERT: B 305 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6557 (m) REVERT: B 340 ARG cc_start: 0.6083 (mmm160) cc_final: 0.5818 (mmm160) REVERT: B 346 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5947 (m-30) REVERT: B 408 ARG cc_start: 0.6660 (mtt90) cc_final: 0.6432 (mtt-85) outliers start: 19 outliers final: 11 residues processed: 90 average time/residue: 0.8582 time to fit residues: 82.5854 Evaluate side-chains 87 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.193804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.174318 restraints weight = 6262.337| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 1.80 r_work: 0.4452 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4327 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6327 Z= 0.214 Angle : 0.631 12.174 8618 Z= 0.321 Chirality : 0.046 0.164 964 Planarity : 0.005 0.040 1107 Dihedral : 4.414 18.192 848 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.99 % Allowed : 21.97 % Favored : 75.04 % 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: -0.26 (0.31), residues: 759 helix: 0.35 (0.32), residues: 265 sheet: 0.30 (0.36), residues: 204 loop : -0.88 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 468 HIS 0.006 0.001 HIS A 416 PHE 0.021 0.002 PHE B 268 TYR 0.028 0.002 TYR B 291 ARG 0.006 0.000 ARG B 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.80 seconds wall clock time: 48 minutes 10.84 seconds (2890.84 seconds total)