Starting phenix.real_space_refine on Tue Jun 25 00:49:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/06_2024/8s86_19798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/06_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_19798/06_2024/8s86_19798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/06_2024/8s86_19798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/06_2024/8s86_19798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s86_19798/06_2024/8s86_19798.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 5.21, per 1000 atoms: 0.84 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: 3.06 Conformation dependent library (CDL) restraints added in 1.1 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: 0.77 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: 1.85 Time building geometry restraints manager: 3.28 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 2.520 nonbonded pdb=" NH1 ARG B 466 " pdb=" OD1 ASP B 467 " model vdw 2.301 2.520 nonbonded pdb=" NE1 TRP B 265 " pdb=" O PRO B 298 " model vdw 2.338 2.520 nonbonded pdb=" N ASP B 191 " pdb=" OD1 ASP B 191 " model vdw 2.372 2.520 nonbonded pdb=" NH1 ARG A 466 " pdb=" OD1 ASP A 467 " model vdw 2.373 2.520 ... (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 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: 3.690 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: 5.990 Check model and map are aligned: 0.180 Set scattering table: 0.070 Process input model: 24.120 Find NCS groups from input model: 0.370 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.520 ------------------------------------------------------------------------------- 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 : 0.806 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: 0.9889 time to fit residues: 153.6998 Evaluate side-chains 93 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 0.2980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN B 117 HIS B 201 HIS B 218 ASN B 416 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.2326 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= 0.200 Angle : 0.650 8.408 8618 Z= 0.336 Chirality : 0.044 0.160 964 Planarity : 0.005 0.047 1107 Dihedral : 5.093 17.025 850 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.74 % Allowed : 14.80 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.29), residues: 759 helix: -0.17 (0.30), residues: 271 sheet: 0.22 (0.36), residues: 207 loop : -1.22 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 205 HIS 0.005 0.001 HIS A 416 PHE 0.014 0.002 PHE B 204 TYR 0.025 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 132 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3544 (OUTLIER) cc_final: 0.3210 (p) REVERT: A 167 LYS cc_start: 0.6457 (tttp) cc_final: 0.6088 (pttp) REVERT: A 228 LYS cc_start: 0.6174 (tttm) cc_final: 0.5475 (ttmm) REVERT: A 234 MET cc_start: 0.6946 (ttm) cc_final: 0.6643 (ttm) REVERT: A 276 GLU cc_start: 0.5537 (mt-10) cc_final: 0.5326 (mt-10) REVERT: B 107 GLN cc_start: 0.6938 (mt0) cc_final: 0.6734 (mt0) REVERT: B 219 MET cc_start: 0.7218 (tpt) cc_final: 0.6910 (tpp) REVERT: B 272 ARG cc_start: 0.6475 (mpp-170) cc_final: 0.6214 (mpp80) REVERT: B 327 MET cc_start: 0.6297 (ttt) cc_final: 0.5820 (tpp) outliers start: 25 outliers final: 6 residues processed: 124 average time/residue: 0.9986 time to fit residues: 131.0405 Evaluate side-chains 95 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 380 SER 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: 0.9980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.0020 chunk 53 optimal weight: 0.5980 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6327 Z= 0.208 Angle : 0.621 8.810 8618 Z= 0.319 Chirality : 0.044 0.138 964 Planarity : 0.005 0.047 1107 Dihedral : 4.600 16.000 848 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.78 % Allowed : 16.14 % Favored : 79.07 % 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: 0.05 (0.30), residues: 276 sheet: 0.29 (0.36), residues: 209 loop : -1.06 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 205 HIS 0.006 0.001 HIS A 416 PHE 0.019 0.003 PHE B 212 TYR 0.026 0.002 TYR A 291 ARG 0.011 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 122 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3388 (OUTLIER) cc_final: 0.3029 (p) REVERT: A 160 ASN cc_start: 0.6682 (t0) cc_final: 0.6455 (t0) REVERT: A 234 MET cc_start: 0.7155 (ttm) cc_final: 0.6883 (tpp) REVERT: A 242 ARG cc_start: 0.6019 (ttm110) cc_final: 0.5587 (ttm110) REVERT: A 276 GLU cc_start: 0.5844 (mt-10) cc_final: 0.5624 (mt-10) REVERT: A 385 ARG cc_start: 0.6039 (mtt180) cc_final: 0.5670 (mtm180) REVERT: B 272 ARG cc_start: 0.6555 (mpp-170) cc_final: 0.6284 (pmm-80) REVERT: B 273 TYR cc_start: 0.6518 (m-10) cc_final: 0.6252 (m-10) REVERT: B 327 MET cc_start: 0.5981 (ttt) cc_final: 0.5699 (tpp) REVERT: B 340 ARG cc_start: 0.6204 (mmm160) cc_final: 0.5466 (tpt170) REVERT: B 371 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5640 (pm20) REVERT: B 420 MET cc_start: 0.6293 (ttp) cc_final: 0.6038 (ttm) outliers start: 32 outliers final: 9 residues processed: 113 average time/residue: 0.9664 time to fit residues: 116.0059 Evaluate side-chains 91 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 380 SER 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: 3.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 71 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.3322 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 : 0.605 7.220 8618 Z= 0.313 Chirality : 0.044 0.149 964 Planarity : 0.005 0.046 1107 Dihedral : 4.485 15.982 848 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.63 % Allowed : 17.49 % Favored : 77.88 % 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: -0.15 (0.30), residues: 759 helix: 0.35 (0.31), residues: 265 sheet: 0.49 (0.36), residues: 200 loop : -0.83 (0.36), residues: 294 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 0.023 0.003 PHE B 398 TYR 0.026 0.002 TYR A 291 ARG 0.003 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 114 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3420 (OUTLIER) cc_final: 0.3058 (p) REVERT: A 234 MET cc_start: 0.7206 (ttm) cc_final: 0.6954 (tpp) REVERT: A 242 ARG cc_start: 0.5952 (ttm110) cc_final: 0.5539 (ttm110) REVERT: A 276 GLU cc_start: 0.6113 (mt-10) cc_final: 0.5864 (pt0) REVERT: A 385 ARG cc_start: 0.6029 (mtt180) cc_final: 0.5637 (mtm180) REVERT: B 242 ARG cc_start: 0.6390 (mtt-85) cc_final: 0.6089 (ptp-110) REVERT: B 272 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6339 (pmm-80) outliers start: 31 outliers final: 14 residues processed: 105 average time/residue: 0.9427 time to fit residues: 105.3285 Evaluate side-chains 94 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 153 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 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: 0.0970 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6327 Z= 0.201 Angle : 0.588 6.731 8618 Z= 0.304 Chirality : 0.044 0.154 964 Planarity : 0.004 0.044 1107 Dihedral : 4.379 15.615 848 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.78 % Allowed : 18.39 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 759 helix: 0.49 (0.32), residues: 259 sheet: 0.41 (0.36), residues: 203 loop : -0.89 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 205 HIS 0.005 0.001 HIS A 416 PHE 0.024 0.003 PHE B 398 TYR 0.030 0.002 TYR A 291 ARG 0.011 0.000 ARG B 340 *********************** 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 119 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.3370 (OUTLIER) cc_final: 0.3021 (p) REVERT: A 234 MET cc_start: 0.7267 (ttm) cc_final: 0.6956 (tpp) REVERT: A 242 ARG cc_start: 0.5932 (ttm110) cc_final: 0.5695 (mmt90) REVERT: A 385 ARG cc_start: 0.6075 (mtt180) cc_final: 0.5636 (mtm180) REVERT: B 94 ASP cc_start: 0.4441 (p0) cc_final: 0.4214 (p0) REVERT: B 180 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5117 (mp) REVERT: B 242 ARG cc_start: 0.6414 (mtt-85) cc_final: 0.6170 (ptp-110) REVERT: B 340 ARG cc_start: 0.6096 (mmm160) cc_final: 0.5703 (mmm160) outliers start: 32 outliers final: 12 residues processed: 112 average time/residue: 1.0372 time to fit residues: 123.6906 Evaluate side-chains 91 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 153 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 380 SER Chi-restraints excluded: chain B residue 475 ASP 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: 0.0670 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6327 Z= 0.230 Angle : 0.624 6.966 8618 Z= 0.320 Chirality : 0.045 0.150 964 Planarity : 0.004 0.040 1107 Dihedral : 4.443 15.987 848 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.63 % Allowed : 18.83 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 759 helix: 0.51 (0.32), residues: 259 sheet: 0.50 (0.37), residues: 199 loop : -0.73 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 205 HIS 0.006 0.001 HIS A 416 PHE 0.025 0.003 PHE B 398 TYR 0.026 0.002 TYR B 291 ARG 0.007 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: 31 poor density : 79 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.3539 (OUTLIER) cc_final: 0.3185 (p) REVERT: A 234 MET cc_start: 0.7321 (ttm) cc_final: 0.7012 (tpp) REVERT: A 242 ARG cc_start: 0.5984 (ttm110) cc_final: 0.5751 (mmt90) REVERT: A 276 GLU cc_start: 0.6334 (pt0) cc_final: 0.5410 (pp20) REVERT: A 327 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5155 (ttp) REVERT: A 374 MET cc_start: 0.6301 (ptm) cc_final: 0.5992 (ptp) REVERT: A 385 ARG cc_start: 0.6190 (mtt180) cc_final: 0.5745 (ttm170) REVERT: B 94 ASP cc_start: 0.4567 (p0) cc_final: 0.4292 (p0) REVERT: B 104 SER cc_start: 0.5374 (m) cc_final: 0.4877 (p) REVERT: B 180 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5197 (mp) REVERT: B 197 HIS cc_start: 0.5915 (m-70) cc_final: 0.5601 (m-70) REVERT: B 340 ARG cc_start: 0.6100 (mmm160) cc_final: 0.5731 (mmm160) outliers start: 31 outliers final: 17 residues processed: 105 average time/residue: 0.9173 time to fit residues: 102.5136 Evaluate side-chains 95 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 VAL 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 475 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN 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 279 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 475 ASP 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: 0.5980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6327 Z= 0.236 Angle : 0.628 7.112 8618 Z= 0.323 Chirality : 0.045 0.153 964 Planarity : 0.005 0.044 1107 Dihedral : 4.513 16.070 848 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.33 % Allowed : 19.43 % Favored : 76.23 % 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: -0.10 (0.31), residues: 759 helix: 0.47 (0.32), residues: 262 sheet: 0.45 (0.37), residues: 201 loop : -0.81 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 205 HIS 0.005 0.001 HIS A 416 PHE 0.022 0.003 PHE B 398 TYR 0.029 0.002 TYR B 291 ARG 0.012 0.001 ARG A 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 106 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 77 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3536 (OUTLIER) cc_final: 0.3184 (p) REVERT: A 180 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.4914 (mp) REVERT: A 234 MET cc_start: 0.7343 (ttm) cc_final: 0.7028 (tpp) REVERT: A 242 ARG cc_start: 0.6035 (ttm110) cc_final: 0.5799 (mmt90) REVERT: A 276 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5526 (pp20) REVERT: A 327 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.4859 (ttp) REVERT: A 374 MET cc_start: 0.6296 (ptm) cc_final: 0.5913 (ptp) REVERT: A 385 ARG cc_start: 0.6157 (mtt180) cc_final: 0.5751 (ttm170) REVERT: B 94 ASP cc_start: 0.4579 (p0) cc_final: 0.4325 (p0) REVERT: B 104 SER cc_start: 0.5434 (m) cc_final: 0.4931 (p) REVERT: B 180 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5241 (mp) REVERT: B 197 HIS cc_start: 0.6170 (m-70) cc_final: 0.5868 (m90) REVERT: B 273 TYR cc_start: 0.6881 (m-10) cc_final: 0.6606 (m-10) REVERT: B 305 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6672 (m) REVERT: B 408 ARG cc_start: 0.6661 (mtt90) cc_final: 0.6423 (mtt-85) REVERT: B 449 THR cc_start: 0.5795 (p) cc_final: 0.5553 (p) outliers start: 29 outliers final: 15 residues processed: 100 average time/residue: 0.9275 time to fit residues: 98.7022 Evaluate side-chains 96 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 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 279 MET Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN 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 279 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 489 LEU 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: 1.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6327 Z= 0.303 Angle : 0.682 7.742 8618 Z= 0.351 Chirality : 0.047 0.178 964 Planarity : 0.005 0.049 1107 Dihedral : 4.793 16.761 848 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.63 % Allowed : 20.33 % 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: -0.24 (0.30), residues: 759 helix: 0.37 (0.32), residues: 259 sheet: 0.35 (0.37), residues: 200 loop : -0.89 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.007 0.001 HIS A 388 PHE 0.028 0.003 PHE B 398 TYR 0.030 0.003 TYR B 291 ARG 0.012 0.001 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 108 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.3562 (OUTLIER) cc_final: 0.3256 (p) REVERT: A 180 LEU cc_start: 0.5433 (OUTLIER) cc_final: 0.4892 (mp) REVERT: A 234 MET cc_start: 0.7348 (ttm) cc_final: 0.7051 (tpp) REVERT: A 246 LYS cc_start: 0.4899 (ttpt) cc_final: 0.4371 (tmmt) REVERT: A 276 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5805 (pp20) REVERT: A 374 MET cc_start: 0.6361 (ptm) cc_final: 0.6030 (ptp) REVERT: A 385 ARG cc_start: 0.6044 (mtt180) cc_final: 0.5652 (ttm170) REVERT: B 94 ASP cc_start: 0.4726 (p0) cc_final: 0.4464 (p0) REVERT: B 104 SER cc_start: 0.5609 (m) cc_final: 0.5158 (p) REVERT: B 197 HIS cc_start: 0.6132 (m-70) cc_final: 0.5855 (m90) REVERT: B 305 THR cc_start: 0.6984 (OUTLIER) cc_final: 0.6719 (m) REVERT: B 340 ARG cc_start: 0.5972 (mmm160) cc_final: 0.5684 (mmm160) REVERT: B 371 GLU cc_start: 0.5677 (tp30) cc_final: 0.5411 (mp0) REVERT: B 408 ARG cc_start: 0.6722 (mtt90) cc_final: 0.6498 (mtt-85) outliers start: 31 outliers final: 20 residues processed: 103 average time/residue: 1.0045 time to fit residues: 109.7430 Evaluate side-chains 94 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 LYS 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 380 SER Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 207 VAL 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 380 SER Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 475 ASP 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: 0.0270 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.0010 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6327 Z= 0.181 Angle : 0.586 6.571 8618 Z= 0.301 Chirality : 0.044 0.146 964 Planarity : 0.004 0.047 1107 Dihedral : 4.314 15.394 848 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.14 % Allowed : 21.52 % Favored : 75.34 % 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: 0.01 (0.31), residues: 759 helix: 0.61 (0.32), residues: 265 sheet: 0.41 (0.37), residues: 204 loop : -0.75 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.009 0.001 HIS A 388 PHE 0.019 0.002 PHE B 398 TYR 0.030 0.002 TYR B 291 ARG 0.010 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 105 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 THR cc_start: 0.3571 (OUTLIER) cc_final: 0.3220 (p) REVERT: A 180 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.4863 (mp) REVERT: A 234 MET cc_start: 0.7230 (ttm) cc_final: 0.6929 (tpp) REVERT: A 346 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6070 (m-30) REVERT: A 374 MET cc_start: 0.6410 (ptm) cc_final: 0.6031 (ptp) REVERT: A 385 ARG cc_start: 0.6056 (mtt180) cc_final: 0.5725 (ttm170) REVERT: B 94 ASP cc_start: 0.4598 (p0) cc_final: 0.4319 (p0) REVERT: B 104 SER cc_start: 0.5502 (m) cc_final: 0.5227 (p) REVERT: B 197 HIS cc_start: 0.6088 (m-70) cc_final: 0.5824 (m90) REVERT: B 243 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6951 (t0) REVERT: B 340 ARG cc_start: 0.5971 (mmm160) cc_final: 0.5611 (mmm160) REVERT: B 346 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.5948 (m-30) REVERT: B 371 GLU cc_start: 0.5692 (tp30) cc_final: 0.5478 (mp0) REVERT: B 408 ARG cc_start: 0.6617 (mtt90) cc_final: 0.6356 (mtt-85) outliers start: 21 outliers final: 10 residues processed: 100 average time/residue: 0.8615 time to fit residues: 92.1328 Evaluate side-chains 88 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS ** 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: 0.6077 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6327 Z= 0.253 Angle : 0.643 7.154 8618 Z= 0.332 Chirality : 0.046 0.168 964 Planarity : 0.005 0.047 1107 Dihedral : 4.541 16.330 848 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.59 % Allowed : 21.67 % Favored : 74.74 % 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: -0.10 (0.31), residues: 759 helix: 0.64 (0.32), residues: 259 sheet: 0.30 (0.37), residues: 202 loop : -0.85 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 468 HIS 0.010 0.001 HIS A 388 PHE 0.023 0.003 PHE B 398 TYR 0.043 0.003 TYR B 273 ARG 0.011 0.001 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 96 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.3545 (OUTLIER) cc_final: 0.3238 (p) REVERT: A 180 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.4859 (mp) REVERT: A 208 ASP cc_start: 0.7367 (m-30) cc_final: 0.7031 (m-30) REVERT: A 234 MET cc_start: 0.7317 (ttm) cc_final: 0.7019 (tpp) REVERT: A 374 MET cc_start: 0.6363 (ptm) cc_final: 0.6027 (ptp) REVERT: A 385 ARG cc_start: 0.6015 (mtt180) cc_final: 0.5659 (ttm170) REVERT: A 475 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.5948 (m-30) REVERT: A 476 LEU cc_start: 0.6838 (tp) cc_final: 0.6414 (mt) REVERT: B 94 ASP cc_start: 0.4628 (p0) cc_final: 0.4363 (p0) REVERT: B 104 SER cc_start: 0.5477 (m) cc_final: 0.5243 (p) REVERT: B 197 HIS cc_start: 0.6097 (m-70) cc_final: 0.5817 (m90) REVERT: B 305 THR cc_start: 0.6868 (OUTLIER) cc_final: 0.6628 (m) REVERT: B 340 ARG cc_start: 0.6079 (mmm160) cc_final: 0.5764 (mmm160) REVERT: B 408 ARG cc_start: 0.6628 (mtt90) cc_final: 0.6364 (mtt-85) outliers start: 24 outliers final: 12 residues processed: 93 average time/residue: 0.9666 time to fit residues: 95.7073 Evaluate side-chains 84 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 136 THR 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 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.186515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.166718 restraints weight = 6404.928| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 1.85 r_work: 0.4379 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4252 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6327 Z= 0.283 Angle : 0.667 7.064 8618 Z= 0.346 Chirality : 0.047 0.185 964 Planarity : 0.005 0.047 1107 Dihedral : 4.700 16.504 848 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.44 % Allowed : 22.42 % Favored : 74.14 % 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: 0.49 (0.32), residues: 259 sheet: 0.17 (0.37), residues: 202 loop : -1.00 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 468 HIS 0.010 0.001 HIS A 388 PHE 0.027 0.003 PHE B 398 TYR 0.031 0.003 TYR B 291 ARG 0.010 0.001 ARG B 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2756.99 seconds wall clock time: 49 minutes 20.34 seconds (2960.34 seconds total)