Starting phenix.real_space_refine on Sun Aug 4 16:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyz_38784/08_2024/8xyz_38784.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyz_38784/08_2024/8xyz_38784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyz_38784/08_2024/8xyz_38784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyz_38784/08_2024/8xyz_38784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyz_38784/08_2024/8xyz_38784.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xyz_38784/08_2024/8xyz_38784.cif" } resolution = 2.96 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5732 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4112 2.51 5 N 1067 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6429 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4885 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.64 Number of scatterers: 6429 At special positions: 0 Unit cell: (75.21, 86.25, 122.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1212 8.00 N 1067 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.43 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.63 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 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: 1492 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 57.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.535A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.291A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.211A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.574A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.163A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.149A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.528A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.567A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.869A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.142A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) 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 283 removed outlier: 3.563A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix removed outlier: 4.010A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.761A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 413 removed outlier: 4.545A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.637A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.615A pdb=" N ALA A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.486A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.509A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.754A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.580A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.599A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.600A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.736A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 876 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: 1.40 Time building geometry restraints manager: 2.62 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: 1661 1.33 - 1.45: 1413 1.45 - 1.57: 3481 1.57 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 6614 Sorted by residual: bond pdb=" C TYR A 215 " pdb=" N ASN A 216 " ideal model delta sigma weight residual 1.330 1.226 0.103 1.37e-02 5.33e+03 5.68e+01 bond pdb=" C ASN A 216 " pdb=" N TYR A 217 " ideal model delta sigma weight residual 1.331 1.254 0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C TYR A 83 " pdb=" N PRO A 84 " ideal model delta sigma weight residual 1.331 1.389 -0.058 1.27e-02 6.20e+03 2.08e+01 bond pdb=" CA LYS B 386 " pdb=" C LYS B 386 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.29e-02 6.01e+03 1.57e+01 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.523 1.568 -0.045 1.19e-02 7.06e+03 1.42e+01 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.91: 143 104.91 - 112.20: 3051 112.20 - 119.48: 2268 119.48 - 126.77: 3398 126.77 - 134.06: 131 Bond angle restraints: 8991 Sorted by residual: angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 111.36 121.55 -10.19 1.09e+00 8.42e-01 8.75e+01 angle pdb=" N ALA B 520 " pdb=" CA ALA B 520 " pdb=" C ALA B 520 " ideal model delta sigma weight residual 108.25 97.62 10.63 1.16e+00 7.43e-01 8.39e+01 angle pdb=" N THR B 523 " pdb=" CA THR B 523 " pdb=" C THR B 523 " ideal model delta sigma weight residual 111.07 119.59 -8.52 1.07e+00 8.73e-01 6.33e+01 angle pdb=" N LEU A 591 " pdb=" CA LEU A 591 " pdb=" C LEU A 591 " ideal model delta sigma weight residual 111.36 103.01 8.35 1.09e+00 8.42e-01 5.86e+01 angle pdb=" N THR A 82 " pdb=" CA THR A 82 " pdb=" C THR A 82 " ideal model delta sigma weight residual 111.28 119.42 -8.14 1.09e+00 8.42e-01 5.57e+01 ... (remaining 8986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3222 17.40 - 34.81: 468 34.81 - 52.21: 154 52.21 - 69.61: 36 69.61 - 87.02: 13 Dihedral angle restraints: 3893 sinusoidal: 1566 harmonic: 2327 Sorted by residual: dihedral pdb=" N CYS B 525 " pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta harmonic sigma weight residual 122.80 112.36 10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N ASP A 338 " pdb=" C ASP A 338 " pdb=" CA ASP A 338 " pdb=" CB ASP A 338 " ideal model delta harmonic sigma weight residual 122.80 133.06 -10.26 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C GLU A 145 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " pdb=" CB GLU A 145 " ideal model delta harmonic sigma weight residual -122.60 -132.52 9.92 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 829 0.094 - 0.188: 74 0.188 - 0.283: 20 0.283 - 0.377: 7 0.377 - 0.471: 3 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA GLU A 145 " pdb=" N GLU A 145 " pdb=" C GLU A 145 " pdb=" CB GLU A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASP A 338 " pdb=" N ASP A 338 " pdb=" C ASP A 338 " pdb=" CB ASP A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA THR A 82 " pdb=" N THR A 82 " pdb=" C THR A 82 " pdb=" CB THR A 82 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 930 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 524 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C VAL B 524 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B 524 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS B 525 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 209 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" CD GLU A 209 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU A 209 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 209 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 335 " 0.039 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 336 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.032 5.00e-02 4.00e+02 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 93 2.62 - 3.19: 5637 3.19 - 3.76: 9504 3.76 - 4.33: 12327 4.33 - 4.90: 20435 Nonbonded interactions: 47996 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.056 2.230 nonbonded pdb=" OD1 ASP A 303 " pdb=" N ALA A 304 " model vdw 2.147 3.120 nonbonded pdb=" O ASN A 194 " pdb=" OD1 ASN A 194 " model vdw 2.201 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN B 334 " pdb=" O ASN B 360 " model vdw 2.292 3.120 ... (remaining 47991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.320 Find NCS groups from input model: 0.060 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:16.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.006 0.103 6614 Z= 0.354 Angle : 1.021 11.924 8991 Z= 0.653 Chirality : 0.069 0.471 933 Planarity : 0.006 0.083 1166 Dihedral : 19.008 87.018 2395 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.91 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 40.11 % Favored : 58.02 % 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: 0.97 (0.29), residues: 787 helix: 1.73 (0.26), residues: 397 sheet: 2.02 (0.82), residues: 31 loop : -0.75 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.005 0.001 HIS A 374 PHE 0.026 0.002 PHE A 314 TYR 0.026 0.002 TYR A 521 ARG 0.018 0.001 ARG A 115 *********************** 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 224 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 0.707 Fit side-chains REVERT: A 194 ASN cc_start: 0.7989 (t0) cc_final: 0.7747 (t0) outliers start: 13 outliers final: 7 residues processed: 218 average time/residue: 0.9660 time to fit residues: 222.6233 Evaluate side-chains 207 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.0030 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 409 GLN B 414 GLN B 422 ASN B 501 ASN A 33 ASN A 60 GLN A 96 GLN A 101 GLN A 117 ASN A 134 ASN A 300 GLN A 442 GLN A 508 ASN A 535 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6614 Z= 0.256 Angle : 0.623 9.234 8991 Z= 0.325 Chirality : 0.044 0.147 933 Planarity : 0.005 0.044 1166 Dihedral : 5.479 51.066 876 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.03 % Favored : 97.84 % Rotamer: Outliers : 5.59 % Allowed : 31.81 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 787 helix: 1.91 (0.26), residues: 408 sheet: 1.97 (0.86), residues: 31 loop : -0.78 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 228 PHE 0.022 0.002 PHE B 497 TYR 0.015 0.002 TYR A 521 ARG 0.003 0.000 ARG A 600 *********************** 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 232 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 495 TYR cc_start: 0.8324 (m-80) cc_final: 0.8029 (m-80) REVERT: A 115 ARG cc_start: 0.7632 (tpm-80) cc_final: 0.7395 (tpt90) REVERT: A 131 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7956 (mmtm) REVERT: A 162 LEU cc_start: 0.8584 (tm) cc_final: 0.8319 (tt) REVERT: A 194 ASN cc_start: 0.8181 (t0) cc_final: 0.7847 (t0) REVERT: A 595 LEU cc_start: 0.7927 (mp) cc_final: 0.7719 (mt) outliers start: 39 outliers final: 10 residues processed: 211 average time/residue: 1.0015 time to fit residues: 223.1853 Evaluate side-chains 193 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 545 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN A 33 ASN A 101 GLN A 300 GLN A 442 GLN A 508 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6614 Z= 0.203 Angle : 0.568 7.717 8991 Z= 0.295 Chirality : 0.042 0.135 933 Planarity : 0.004 0.041 1166 Dihedral : 4.714 39.957 869 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.01 % Allowed : 31.52 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.30), residues: 787 helix: 2.06 (0.26), residues: 404 sheet: 2.18 (0.86), residues: 29 loop : -0.82 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE B 497 TYR 0.016 0.001 TYR A 50 ARG 0.004 0.000 ARG A 600 *********************** 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 221 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: B 495 TYR cc_start: 0.8266 (m-80) cc_final: 0.7971 (m-80) REVERT: A 162 LEU cc_start: 0.8592 (tm) cc_final: 0.8319 (tt) REVERT: A 184 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 194 ASN cc_start: 0.8225 (t0) cc_final: 0.7814 (t0) REVERT: A 331 SER cc_start: 0.8209 (p) cc_final: 0.7939 (p) outliers start: 35 outliers final: 16 residues processed: 202 average time/residue: 1.0171 time to fit residues: 216.9240 Evaluate side-chains 199 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 430 GLU 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: 4.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 53 ASN A 58 ASN A 101 GLN A 300 GLN A 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6614 Z= 0.366 Angle : 0.628 8.026 8991 Z= 0.336 Chirality : 0.046 0.151 933 Planarity : 0.005 0.042 1166 Dihedral : 4.859 31.700 869 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.73 % Allowed : 32.52 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.30), residues: 787 helix: 1.93 (0.27), residues: 408 sheet: 1.87 (0.83), residues: 29 loop : -0.89 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.035 0.002 PHE B 497 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.000 ARG A 600 *********************** 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 238 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 0.649 Fit side-chains REVERT: B 493 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 495 TYR cc_start: 0.8299 (m-80) cc_final: 0.8066 (m-80) REVERT: A 42 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: A 162 LEU cc_start: 0.8686 (tm) cc_final: 0.8444 (tt) REVERT: A 194 ASN cc_start: 0.8304 (t0) cc_final: 0.7922 (t0) REVERT: A 502 SER cc_start: 0.8131 (p) cc_final: 0.7921 (p) outliers start: 40 outliers final: 17 residues processed: 216 average time/residue: 0.8172 time to fit residues: 186.5966 Evaluate side-chains 214 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 522 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 chunk 0 optimal weight: 40.0000 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 300 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6614 Z= 0.172 Angle : 0.548 5.554 8991 Z= 0.289 Chirality : 0.040 0.145 933 Planarity : 0.004 0.037 1166 Dihedral : 4.333 16.652 865 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.87 % Allowed : 33.95 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.30), residues: 787 helix: 2.02 (0.27), residues: 411 sheet: 2.01 (0.85), residues: 29 loop : -0.76 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.029 0.001 PHE B 497 TYR 0.017 0.001 TYR A 50 ARG 0.002 0.000 ARG A 357 *********************** 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 214 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8024 (tttm) cc_final: 0.7772 (tttm) REVERT: B 497 PHE cc_start: 0.7685 (m-80) cc_final: 0.7409 (m-80) REVERT: A 162 LEU cc_start: 0.8546 (tm) cc_final: 0.8285 (tt) REVERT: A 184 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8366 (p) REVERT: A 189 GLU cc_start: 0.7462 (tp30) cc_final: 0.7163 (tp30) REVERT: A 331 SER cc_start: 0.8250 (p) cc_final: 0.7942 (p) outliers start: 34 outliers final: 13 residues processed: 203 average time/residue: 1.0509 time to fit residues: 224.9453 Evaluate side-chains 196 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 582 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 194 ASN A 300 GLN A 442 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6614 Z= 0.296 Angle : 0.606 7.241 8991 Z= 0.322 Chirality : 0.043 0.137 933 Planarity : 0.004 0.038 1166 Dihedral : 4.462 18.444 865 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.59 % Allowed : 33.67 % Favored : 60.74 % 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: 1.13 (0.30), residues: 787 helix: 2.00 (0.27), residues: 408 sheet: 1.80 (0.85), residues: 29 loop : -0.90 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 349 HIS 0.006 0.001 HIS A 374 PHE 0.027 0.001 PHE B 497 TYR 0.015 0.002 TYR A 510 ARG 0.002 0.000 ARG A 518 *********************** 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 231 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 0.648 Fit side-chains REVERT: B 493 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: B 497 PHE cc_start: 0.7757 (m-80) cc_final: 0.7525 (m-80) REVERT: A 42 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 115 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7300 (tpt-90) REVERT: A 162 LEU cc_start: 0.8631 (tm) cc_final: 0.8379 (tt) REVERT: A 184 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8391 (p) REVERT: A 189 GLU cc_start: 0.7498 (tp30) cc_final: 0.7170 (tp30) REVERT: A 331 SER cc_start: 0.8251 (p) cc_final: 0.7958 (p) outliers start: 39 outliers final: 19 residues processed: 211 average time/residue: 1.0073 time to fit residues: 224.1242 Evaluate side-chains 210 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 582 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 194 ASN A 300 GLN A 330 ASN A 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6614 Z= 0.210 Angle : 0.591 10.956 8991 Z= 0.306 Chirality : 0.041 0.139 933 Planarity : 0.004 0.036 1166 Dihedral : 4.357 21.200 865 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.87 % Allowed : 35.39 % Favored : 60.74 % 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: 1.23 (0.30), residues: 787 helix: 2.09 (0.27), residues: 404 sheet: 1.96 (0.87), residues: 29 loop : -0.84 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.021 0.001 PHE B 497 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG A 600 *********************** 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 213 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 0.737 Fit side-chains REVERT: B 493 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: A 115 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7242 (tpt-90) REVERT: A 162 LEU cc_start: 0.8594 (tm) cc_final: 0.8336 (tt) REVERT: A 189 GLU cc_start: 0.7484 (tp30) cc_final: 0.7171 (tp30) REVERT: A 470 LYS cc_start: 0.8451 (tppp) cc_final: 0.7973 (ttmp) outliers start: 27 outliers final: 12 residues processed: 202 average time/residue: 1.0465 time to fit residues: 222.7795 Evaluate side-chains 198 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 607 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 117 ASN A 194 ASN A 300 GLN A 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6614 Z= 0.273 Angle : 0.621 11.759 8991 Z= 0.324 Chirality : 0.043 0.141 933 Planarity : 0.004 0.036 1166 Dihedral : 4.439 20.519 865 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.15 % Allowed : 34.81 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.30), residues: 787 helix: 1.97 (0.27), residues: 408 sheet: 1.98 (0.87), residues: 29 loop : -0.85 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.040 0.001 PHE B 497 TYR 0.033 0.002 TYR B 351 ARG 0.004 0.000 ARG A 518 *********************** 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 220 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.688 Fit side-chains REVERT: B 493 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: A 115 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7306 (tpt-90) REVERT: A 162 LEU cc_start: 0.8610 (tm) cc_final: 0.8360 (tt) REVERT: A 189 GLU cc_start: 0.7489 (tp30) cc_final: 0.7197 (tp30) REVERT: A 194 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7938 (t0) REVERT: A 331 SER cc_start: 0.8223 (p) cc_final: 0.7976 (p) REVERT: A 470 LYS cc_start: 0.8414 (tppp) cc_final: 0.8143 (tttp) outliers start: 29 outliers final: 17 residues processed: 204 average time/residue: 1.0176 time to fit residues: 218.9708 Evaluate side-chains 201 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 607 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN A 101 GLN A 194 ASN A 300 GLN A 330 ASN A 442 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6614 Z= 0.192 Angle : 0.589 7.054 8991 Z= 0.309 Chirality : 0.041 0.133 933 Planarity : 0.004 0.035 1166 Dihedral : 4.319 19.798 865 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.30 % Allowed : 36.10 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.30), residues: 787 helix: 2.14 (0.27), residues: 396 sheet: 1.99 (0.88), residues: 29 loop : -0.78 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.033 0.001 PHE B 497 TYR 0.035 0.001 TYR B 351 ARG 0.003 0.000 ARG A 518 *********************** 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 215 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 0.734 Fit side-chains REVERT: B 493 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: A 115 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7195 (tpt-90) REVERT: A 162 LEU cc_start: 0.8566 (tm) cc_final: 0.8312 (tt) REVERT: A 189 GLU cc_start: 0.7446 (tp30) cc_final: 0.7234 (tp30) outliers start: 23 outliers final: 12 residues processed: 204 average time/residue: 0.9716 time to fit residues: 209.5451 Evaluate side-chains 204 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 582 ARG 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: 0.5980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 194 ASN A 300 GLN A 442 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6614 Z= 0.237 Angle : 0.635 11.503 8991 Z= 0.331 Chirality : 0.042 0.133 933 Planarity : 0.004 0.035 1166 Dihedral : 4.341 22.549 865 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 36.53 % Favored : 60.46 % 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: 1.25 (0.30), residues: 787 helix: 2.14 (0.27), residues: 396 sheet: 2.16 (0.89), residues: 29 loop : -0.81 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.017 0.001 PHE B 429 TYR 0.034 0.002 TYR B 351 ARG 0.004 0.000 ARG A 518 ********************** 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 215 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 0.680 Fit side-chains REVERT: B 493 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: A 148 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8284 (mt) REVERT: A 162 LEU cc_start: 0.8572 (tm) cc_final: 0.8339 (tt) REVERT: A 189 GLU cc_start: 0.7451 (tp30) cc_final: 0.7197 (tp30) outliers start: 21 outliers final: 12 residues processed: 208 average time/residue: 1.0080 time to fit residues: 222.0124 Evaluate side-chains 209 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 582 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 439 ASN A 101 GLN A 117 ASN A 194 ASN A 300 GLN A 330 ASN A 442 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109774 restraints weight = 10310.633| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.44 r_work: 0.3346 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6614 Z= 0.203 Angle : 0.609 7.905 8991 Z= 0.323 Chirality : 0.041 0.132 933 Planarity : 0.004 0.036 1166 Dihedral : 4.293 22.888 865 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.87 % Allowed : 37.39 % Favored : 59.74 % 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: 1.26 (0.30), residues: 787 helix: 2.11 (0.27), residues: 395 sheet: 2.26 (0.90), residues: 29 loop : -0.76 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.016 0.001 PHE B 429 TYR 0.034 0.001 TYR B 351 ARG 0.005 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.31 seconds wall clock time: 64 minutes 20.49 seconds (3860.49 seconds total)