Starting phenix.real_space_refine on Mon Mar 11 00:43:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrk_34976/03_2024/8hrk_34976.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrk_34976/03_2024/8hrk_34976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrk_34976/03_2024/8hrk_34976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrk_34976/03_2024/8hrk_34976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrk_34976/03_2024/8hrk_34976.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrk_34976/03_2024/8hrk_34976.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.157 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 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 3.92, per 1000 atoms: 0.61 Number of scatterers: 6412 At special positions: 0 Unit cell: (71.38, 88.58, 126.42, 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 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 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: 2.16 Conformation dependent library (CDL) restraints added in 1.2 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 48.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.720A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.592A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.823A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.740A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.669A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.577A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.549A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.881A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.560A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.248A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.247A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.633A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.543A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.733A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.525A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.168A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.547A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.747A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.749A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.767A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.977A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 389' Processing helix chain 'E' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.451A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.938A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.537A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 511 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.767A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 597 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: 1.56 Time building geometry restraints manager: 2.41 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: 1286 1.33 - 1.45: 1729 1.45 - 1.57: 3516 1.57 - 1.69: 3 1.69 - 1.81: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.503 1.208 0.295 3.40e-02 8.65e+02 7.55e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB PRO A 235 " pdb=" CG PRO A 235 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.59e+00 bond pdb=" CG PRO A 235 " pdb=" CD PRO A 235 " ideal model delta sigma weight residual 1.503 1.416 0.087 3.40e-02 8.65e+02 6.52e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 85.48 - 95.38: 4 95.38 - 105.28: 132 105.28 - 115.18: 3855 115.18 - 125.08: 4827 125.08 - 134.98: 140 Bond angle restraints: 8958 Sorted by residual: angle pdb=" CA PRO A 235 " pdb=" N PRO A 235 " pdb=" CD PRO A 235 " ideal model delta sigma weight residual 112.00 94.20 17.80 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 85.48 17.72 1.50e+00 4.44e-01 1.40e+02 angle pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" N PRO A 235 " pdb=" CD PRO A 235 " pdb=" CG PRO A 235 " ideal model delta sigma weight residual 103.20 93.98 9.22 1.50e+00 4.44e-01 3.77e+01 angle pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 104.50 92.97 11.53 1.90e+00 2.77e-01 3.68e+01 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3337 18.00 - 36.00: 432 36.00 - 53.99: 97 53.99 - 71.99: 19 71.99 - 89.99: 8 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 176.81 -83.81 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 147.88 -54.88 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -44.04 -41.96 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 414 0.024 - 0.049: 319 0.049 - 0.073: 142 0.073 - 0.097: 35 0.097 - 0.121: 24 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA VAL E 511 " pdb=" N VAL E 511 " pdb=" C VAL E 511 " pdb=" CB VAL E 511 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.106 5.00e-02 4.00e+02 1.45e-01 3.34e+01 pdb=" N PRO A 235 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO A 321 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " 0.063 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 415 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.047 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1697 2.80 - 3.32: 5341 3.32 - 3.85: 9886 3.85 - 4.37: 11141 4.37 - 4.90: 19953 Nonbonded interactions: 48018 Sorted by model distance: nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 2.273 2.520 nonbonded pdb=" OE2 GLU A 489 " pdb=" OH TYR A 613 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR E 351 " pdb=" NH2 ARG E 452 " model vdw 2.273 2.520 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.288 2.440 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 362 " model vdw 2.293 2.440 ... (remaining 48013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 7.150 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 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 : 0.005 0.295 6592 Z= 0.389 Angle : 0.711 17.801 8958 Z= 0.444 Chirality : 0.040 0.121 934 Planarity : 0.008 0.145 1165 Dihedral : 16.730 89.990 2384 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.14 % Allowed : 17.87 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.29), residues: 787 helix: -0.48 (0.29), residues: 345 sheet: -2.36 (0.79), residues: 42 loop : -1.69 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 349 HIS 0.001 0.000 HIS A 239 PHE 0.008 0.001 PHE A 369 TYR 0.018 0.001 TYR A 41 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.6793 (tt0) cc_final: 0.6416 (mt-10) REVERT: A 376 MET cc_start: 0.7200 (ttt) cc_final: 0.6910 (ttt) REVERT: E 335 LEU cc_start: 0.0534 (OUTLIER) cc_final: -0.0132 (mm) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1908 time to fit residues: 23.4395 Evaluate side-chains 79 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 432 ASN E 474 GLN E 493 GLN E 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 6592 Z= 0.310 Angle : 0.641 6.236 8958 Z= 0.344 Chirality : 0.046 0.150 934 Planarity : 0.006 0.078 1165 Dihedral : 4.966 47.714 863 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.18 % Allowed : 18.44 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.29), residues: 787 helix: -0.54 (0.29), residues: 333 sheet: -3.52 (0.85), residues: 34 loop : -1.67 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 473 HIS 0.014 0.002 HIS A 241 PHE 0.025 0.002 PHE A 230 TYR 0.021 0.002 TYR A 41 ARG 0.004 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.692 Fit side-chains REVERT: A 35 GLU cc_start: 0.7265 (tt0) cc_final: 0.6844 (mt-10) REVERT: A 131 LYS cc_start: 0.6015 (mmtt) cc_final: 0.4873 (mmmt) REVERT: A 182 GLU cc_start: 0.7161 (tt0) cc_final: 0.6895 (mt-10) REVERT: A 359 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.5161 (tt) REVERT: A 483 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 534 LYS cc_start: 0.8215 (tppt) cc_final: 0.7976 (tppt) REVERT: E 335 LEU cc_start: 0.0764 (OUTLIER) cc_final: 0.0122 (mm) REVERT: E 450 ASN cc_start: 0.7490 (t0) cc_final: 0.7009 (t0) outliers start: 29 outliers final: 12 residues processed: 108 average time/residue: 0.1952 time to fit residues: 27.8550 Evaluate side-chains 86 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 494 SER 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: 3.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 380 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6592 Z= 0.187 Angle : 0.492 4.777 8958 Z= 0.264 Chirality : 0.041 0.133 934 Planarity : 0.005 0.069 1165 Dihedral : 4.364 45.399 863 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.88 % Allowed : 20.32 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.29), residues: 787 helix: -0.25 (0.29), residues: 345 sheet: -2.84 (0.72), residues: 45 loop : -1.64 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.015 0.001 PHE A 327 TYR 0.010 0.001 TYR E 495 ARG 0.006 0.000 ARG E 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.723 Fit side-chains REVERT: A 35 GLU cc_start: 0.7259 (tt0) cc_final: 0.6849 (mt-10) REVERT: A 131 LYS cc_start: 0.6232 (mmtt) cc_final: 0.4858 (mmmt) REVERT: A 182 GLU cc_start: 0.7186 (tt0) cc_final: 0.6869 (mt-10) REVERT: A 360 MET cc_start: 0.1705 (tpp) cc_final: 0.1386 (tpt) REVERT: E 450 ASN cc_start: 0.7575 (t0) cc_final: 0.7133 (t0) outliers start: 20 outliers final: 18 residues processed: 92 average time/residue: 0.1836 time to fit residues: 22.9268 Evaluate side-chains 89 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 511 VAL 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: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS E 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6592 Z= 0.263 Angle : 0.599 6.164 8958 Z= 0.325 Chirality : 0.044 0.215 934 Planarity : 0.005 0.066 1165 Dihedral : 4.597 16.747 861 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.32 % Allowed : 19.31 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.28), residues: 787 helix: -0.52 (0.28), residues: 346 sheet: -1.89 (1.09), residues: 24 loop : -1.87 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 473 HIS 0.013 0.001 HIS A 241 PHE 0.019 0.002 PHE A 230 TYR 0.017 0.002 TYR A 385 ARG 0.005 0.001 ARG E 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7355 (tt0) cc_final: 0.6972 (mt-10) REVERT: A 50 TYR cc_start: 0.7455 (t80) cc_final: 0.7195 (t80) REVERT: A 123 MET cc_start: 0.8294 (mtt) cc_final: 0.7920 (mtm) REVERT: A 131 LYS cc_start: 0.6270 (mmtt) cc_final: 0.4876 (mmmt) REVERT: A 182 GLU cc_start: 0.7164 (tt0) cc_final: 0.6737 (mt-10) REVERT: A 531 GLN cc_start: 0.7763 (tp40) cc_final: 0.7266 (tt0) REVERT: A 571 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: E 335 LEU cc_start: 0.0843 (OUTLIER) cc_final: 0.0133 (mm) REVERT: E 420 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7924 (p0) outliers start: 30 outliers final: 18 residues processed: 104 average time/residue: 0.2042 time to fit residues: 28.1435 Evaluate side-chains 94 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6592 Z= 0.248 Angle : 0.553 4.826 8958 Z= 0.298 Chirality : 0.043 0.173 934 Planarity : 0.005 0.060 1165 Dihedral : 4.494 16.102 861 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.46 % Allowed : 20.61 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.29), residues: 787 helix: -0.31 (0.29), residues: 337 sheet: -2.20 (0.76), residues: 46 loop : -1.80 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 473 HIS 0.008 0.001 HIS A 241 PHE 0.015 0.002 PHE A 400 TYR 0.016 0.002 TYR E 351 ARG 0.005 0.001 ARG E 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7407 (tt0) cc_final: 0.7014 (mt-10) REVERT: A 50 TYR cc_start: 0.7820 (t80) cc_final: 0.7478 (t80) REVERT: A 171 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: A 182 GLU cc_start: 0.7172 (tt0) cc_final: 0.6760 (mt-10) REVERT: A 360 MET cc_start: 0.2804 (tpt) cc_final: 0.0396 (ptm) REVERT: E 335 LEU cc_start: 0.0741 (OUTLIER) cc_final: 0.0078 (mm) outliers start: 24 outliers final: 16 residues processed: 98 average time/residue: 0.1991 time to fit residues: 27.6943 Evaluate side-chains 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6592 Z= 0.188 Angle : 0.510 4.722 8958 Z= 0.274 Chirality : 0.042 0.185 934 Planarity : 0.004 0.053 1165 Dihedral : 4.220 18.968 861 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.31 % Allowed : 21.33 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.29), residues: 787 helix: -0.04 (0.30), residues: 336 sheet: -2.07 (0.77), residues: 46 loop : -1.71 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 473 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE E 486 TYR 0.015 0.001 TYR E 351 ARG 0.008 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.729 Fit side-chains REVERT: A 35 GLU cc_start: 0.7367 (tt0) cc_final: 0.6989 (mt-10) REVERT: A 50 TYR cc_start: 0.7996 (t80) cc_final: 0.7763 (t80) REVERT: A 123 MET cc_start: 0.8338 (mtt) cc_final: 0.8070 (mtm) REVERT: A 182 GLU cc_start: 0.7175 (tt0) cc_final: 0.6764 (mt-10) REVERT: A 360 MET cc_start: 0.2926 (tpt) cc_final: 0.0650 (ptm) REVERT: A 531 GLN cc_start: 0.7439 (tp-100) cc_final: 0.6893 (tt0) REVERT: E 335 LEU cc_start: 0.0744 (OUTLIER) cc_final: 0.0045 (mm) outliers start: 23 outliers final: 17 residues processed: 91 average time/residue: 0.1551 time to fit residues: 19.8188 Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6592 Z= 0.144 Angle : 0.469 4.671 8958 Z= 0.251 Chirality : 0.040 0.164 934 Planarity : 0.004 0.048 1165 Dihedral : 3.899 16.269 861 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.88 % Allowed : 21.18 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.30), residues: 787 helix: 0.31 (0.30), residues: 335 sheet: -1.86 (0.85), residues: 40 loop : -1.60 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.014 0.001 TYR E 351 ARG 0.006 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.722 Fit side-chains REVERT: A 35 GLU cc_start: 0.7387 (tt0) cc_final: 0.7006 (mt-10) REVERT: A 123 MET cc_start: 0.8344 (mtt) cc_final: 0.8088 (mtm) REVERT: A 269 ASP cc_start: 0.8324 (p0) cc_final: 0.8098 (p0) REVERT: A 360 MET cc_start: 0.2853 (tpt) cc_final: 0.0932 (ptm) REVERT: A 531 GLN cc_start: 0.7407 (tp-100) cc_final: 0.6771 (tt0) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.1619 time to fit residues: 21.6519 Evaluate side-chains 84 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 511 VAL 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: 0.3980 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.183 Angle : 0.503 4.879 8958 Z= 0.269 Chirality : 0.041 0.166 934 Planarity : 0.004 0.048 1165 Dihedral : 3.967 15.213 861 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 21.76 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.29), residues: 787 helix: 0.27 (0.30), residues: 335 sheet: -1.63 (0.87), residues: 40 loop : -1.59 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.014 0.001 TYR A 50 ARG 0.004 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.737 Fit side-chains REVERT: A 35 GLU cc_start: 0.7393 (tt0) cc_final: 0.7033 (mt-10) REVERT: A 123 MET cc_start: 0.8304 (mtt) cc_final: 0.8099 (mtm) REVERT: A 360 MET cc_start: 0.3106 (tpt) cc_final: 0.1250 (ptm) REVERT: A 531 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6879 (tt0) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 0.1817 time to fit residues: 23.1541 Evaluate side-chains 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN E 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6592 Z= 0.157 Angle : 0.473 4.821 8958 Z= 0.251 Chirality : 0.041 0.154 934 Planarity : 0.004 0.047 1165 Dihedral : 3.748 14.302 861 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 20.75 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.96 (0.30), residues: 787 helix: 0.50 (0.31), residues: 335 sheet: -1.59 (1.06), residues: 30 loop : -1.55 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.003 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.014 0.001 TYR E 351 ARG 0.008 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.689 Fit side-chains REVERT: A 35 GLU cc_start: 0.7379 (tt0) cc_final: 0.6992 (mt-10) REVERT: A 62 MET cc_start: 0.4885 (mmm) cc_final: 0.4294 (mtm) REVERT: A 123 MET cc_start: 0.8306 (mtt) cc_final: 0.8048 (mtm) REVERT: A 171 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: A 269 ASP cc_start: 0.8303 (p0) cc_final: 0.8039 (p0) REVERT: A 360 MET cc_start: 0.3000 (tpt) cc_final: 0.1666 (ptm) REVERT: A 531 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6769 (tt0) REVERT: E 335 LEU cc_start: 0.1038 (OUTLIER) cc_final: 0.0339 (mm) REVERT: E 439 ASN cc_start: 0.8229 (t0) cc_final: 0.7996 (t0) outliers start: 23 outliers final: 14 residues processed: 97 average time/residue: 0.1952 time to fit residues: 25.9342 Evaluate side-chains 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 0.0070 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6592 Z= 0.149 Angle : 0.476 5.141 8958 Z= 0.253 Chirality : 0.041 0.156 934 Planarity : 0.004 0.046 1165 Dihedral : 3.654 14.260 861 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 21.90 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.87 (0.30), residues: 787 helix: 0.56 (0.31), residues: 335 sheet: -1.47 (1.07), residues: 30 loop : -1.49 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 369 TYR 0.014 0.001 TYR E 351 ARG 0.007 0.000 ARG A 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.762 Fit side-chains REVERT: A 35 GLU cc_start: 0.7397 (tt0) cc_final: 0.7029 (mt-10) REVERT: A 62 MET cc_start: 0.4988 (mmm) cc_final: 0.4456 (mtm) REVERT: A 269 ASP cc_start: 0.8211 (p0) cc_final: 0.7959 (p0) REVERT: A 360 MET cc_start: 0.2979 (tpt) cc_final: 0.1803 (ptm) REVERT: A 531 GLN cc_start: 0.7391 (tp-100) cc_final: 0.6751 (tt0) REVERT: E 335 LEU cc_start: 0.0987 (OUTLIER) cc_final: 0.0294 (mm) REVERT: E 439 ASN cc_start: 0.8256 (t0) cc_final: 0.8021 (t0) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.1703 time to fit residues: 20.2848 Evaluate side-chains 84 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 351 TYR Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.0770 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.185835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147430 restraints weight = 7702.077| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.61 r_work: 0.3520 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6592 Z= 0.146 Angle : 0.472 6.409 8958 Z= 0.251 Chirality : 0.041 0.161 934 Planarity : 0.004 0.046 1165 Dihedral : 3.646 16.534 861 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 21.61 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.76 (0.30), residues: 787 helix: 0.64 (0.31), residues: 335 sheet: -1.32 (1.08), residues: 30 loop : -1.43 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.003 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.014 0.001 TYR E 351 ARG 0.007 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.47 seconds wall clock time: 34 minutes 3.32 seconds (2043.32 seconds total)