Starting phenix.real_space_refine on Sun Mar 10 20:27:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/03_2024/7ykj_33892.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/03_2024/7ykj_33892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/03_2024/7ykj_33892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/03_2024/7ykj_33892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/03_2024/7ykj_33892.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/03_2024/7ykj_33892.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.067 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 23 5.16 5 C 3072 2.51 5 N 810 2.21 5 O 906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "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: 4811 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1529 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1556 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 906 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.39, per 1000 atoms: 0.70 Number of scatterers: 4811 At special positions: 0 Unit cell: (73.14, 112.36, 95.4, 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 23 16.00 O 906 8.00 N 810 7.00 C 3072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.06 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.02 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: 1.77 Conformation dependent library (CDL) restraints added in 933.2 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1154 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 13.6% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.828A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.034A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.702A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.538A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.802A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.708A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.379A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.206A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 29 through 33 removed outlier: 4.178A pdb=" N SER D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.990A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.769A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.082A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.017A pdb=" N CYS A 96 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP A 111 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS A 98 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.676A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 333 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: 1.28 Time building geometry restraints manager: 1.93 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: 1077 1.33 - 1.45: 1243 1.45 - 1.58: 2596 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 4941 Sorted by residual: bond pdb=" N ILE D 59 " pdb=" CA ILE D 59 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.74e+01 bond pdb=" CE1 HIS B 505 " pdb=" NE2 HIS B 505 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.70e+01 bond pdb=" CE1 HIS C 505 " pdb=" NE2 HIS C 505 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" N SER B 446 " pdb=" CA SER B 446 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.16e-02 7.43e+03 9.81e+00 ... (remaining 4936 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.81: 125 105.81 - 113.35: 2288 113.35 - 120.89: 2666 120.89 - 128.43: 1629 128.43 - 135.98: 30 Bond angle restraints: 6738 Sorted by residual: angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 98.63 13.37 1.40e+00 5.10e-01 9.12e+01 angle pdb=" OD1 ASN A 74 " pdb=" CG ASN A 74 " pdb=" ND2 ASN A 74 " ideal model delta sigma weight residual 122.60 117.20 5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" OE1 GLN C 409 " pdb=" CD GLN C 409 " pdb=" NE2 GLN C 409 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.70e+01 angle pdb=" OD1 ASN C 439 " pdb=" CG ASN C 439 " pdb=" ND2 ASN C 439 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.70e+01 angle pdb=" OD1 ASN C 394 " pdb=" CG ASN C 394 " pdb=" ND2 ASN C 394 " ideal model delta sigma weight residual 122.60 117.49 5.11 1.00e+00 1.00e+00 2.61e+01 ... (remaining 6733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2552 17.52 - 35.04: 277 35.04 - 52.56: 54 52.56 - 70.08: 12 70.08 - 87.60: 6 Dihedral angle restraints: 2901 sinusoidal: 1082 harmonic: 1819 Sorted by residual: dihedral pdb=" CD ARG B 466 " pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " pdb=" NH1 ARG B 466 " ideal model delta sinusoidal sigma weight residual 0.00 87.60 -87.60 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CA SER D 95 " pdb=" C SER D 95 " pdb=" N PRO D 96 " pdb=" CA PRO D 96 " ideal model delta harmonic sigma weight residual -180.00 -134.01 -45.99 0 5.00e+00 4.00e-02 8.46e+01 dihedral pdb=" CD ARG C 498 " pdb=" NE ARG C 498 " pdb=" CZ ARG C 498 " pdb=" NH1 ARG C 498 " ideal model delta sinusoidal sigma weight residual 0.00 -82.34 82.34 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 2898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 525 0.095 - 0.190: 167 0.190 - 0.285: 31 0.285 - 0.380: 4 0.380 - 0.475: 1 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA THR D 5 " pdb=" N THR D 5 " pdb=" C THR D 5 " pdb=" CB THR D 5 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB THR A 115 " pdb=" CA THR A 115 " pdb=" OG1 THR A 115 " pdb=" CG2 THR A 115 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 725 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 32 " 0.175 2.00e-02 2.50e+03 9.32e-02 1.74e+02 pdb=" CG TYR A 32 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR A 32 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR A 32 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR A 32 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 32 " -0.038 2.00e-02 2.50e+03 pdb=" CZ TYR A 32 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 32 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 109 " 0.061 2.00e-02 2.50e+03 1.26e-01 1.59e+02 pdb=" CG ASP A 109 " -0.218 2.00e-02 2.50e+03 pdb=" OD1 ASP A 109 " 0.079 2.00e-02 2.50e+03 pdb=" OD2 ASP A 109 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 36 " 0.128 2.00e-02 2.50e+03 7.75e-02 1.50e+02 pdb=" CG TRP A 36 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 36 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 36 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP A 36 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TRP A 36 " 0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP A 36 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 36 " 0.107 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 36 " -0.089 2.00e-02 2.50e+03 pdb=" CH2 TRP A 36 " 0.073 2.00e-02 2.50e+03 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 5 2.39 - 3.02: 2646 3.02 - 3.64: 6997 3.64 - 4.27: 10751 4.27 - 4.90: 17483 Nonbonded interactions: 37882 Sorted by model distance: nonbonded pdb=" O TYR C 495 " pdb=" OG SER C 496 " model vdw 1.761 2.440 nonbonded pdb=" OG SER A 101 " pdb=" O TYR A 103 " model vdw 2.026 2.440 nonbonded pdb=" OG1 THR A 54 " pdb=" OD1 ASP A 56 " model vdw 2.284 2.440 nonbonded pdb=" O PRO D 96 " pdb=" N LEU D 98 " model vdw 2.286 2.520 nonbonded pdb=" NH1 ARG D 55 " pdb=" O PHE D 63 " model vdw 2.356 2.520 ... (remaining 37877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 331 through 374 or (resid 375 through 377 and (name N or n \ ame CA or name C or name O or name CB )) or resid 378 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 49 \ 2 or (resid 493 and (name N or name CA or name C or name O or name CB )) or resi \ d 494 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ me CB )) or resid 518 through 528)) selection = (chain 'C' and (resid 331 through 345 or (resid 346 through 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 357 or (resid 358 \ and (name N or name CA or name C or name O or name CB )) or resid 359 through 37 \ 5 or (resid 376 through 377 and (name N or name CA or name C or name O or name C \ B )) or resid 378 through 423 or (resid 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 through 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 445 or (resid 446 and \ (name N or name CA or name C or name O or name CB )) or resid 447 through 451 or \ (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 3 through 480 or (resid 481 and (name N or name CA or name C or name O or name C \ B )) or resid 482 through 495 or (resid 496 and (name N or name CA or name C or \ name O or name CB )) or resid 497 or (resid 498 and (name N or name CA or name C \ or name O or name CB )) or resid 499 through 528)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.000 Extract box with map and model: 7.060 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.870 Find NCS groups from input model: 0.230 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 : 0.013 0.058 4941 Z= 0.844 Angle : 1.781 13.371 6738 Z= 1.182 Chirality : 0.095 0.475 728 Planarity : 0.040 0.488 878 Dihedral : 15.542 87.598 1720 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 1.13 % Allowed : 6.63 % Favored : 92.23 % Rotamer: Outliers : 2.98 % Allowed : 16.70 % Favored : 80.32 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.31), residues: 618 helix: -4.60 (0.38), residues: 42 sheet: -1.24 (0.41), residues: 148 loop : -1.57 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.128 0.026 TRP A 36 HIS 0.019 0.004 HIS A 59 PHE 0.045 0.008 PHE A 27 TYR 0.175 0.020 TYR A 32 ARG 0.040 0.003 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.549 Fit side-chains REVERT: B 400 PHE cc_start: 0.6246 (p90) cc_final: 0.5878 (p90) REVERT: A 28 THR cc_start: 0.9157 (m) cc_final: 0.8909 (p) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 0.2452 time to fit residues: 38.4070 Evaluate side-chains 89 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4941 Z= 0.197 Angle : 0.647 7.013 6738 Z= 0.338 Chirality : 0.046 0.192 728 Planarity : 0.006 0.064 878 Dihedral : 5.964 40.989 702 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 4.69 % Favored : 94.50 % Rotamer: Outliers : 5.37 % Allowed : 17.69 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.34), residues: 618 helix: -3.83 (0.50), residues: 43 sheet: -1.16 (0.38), residues: 152 loop : -0.75 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.004 0.001 HIS C 519 PHE 0.012 0.001 PHE D 100 TYR 0.014 0.002 TYR A 95 ARG 0.004 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.568 Fit side-chains REVERT: B 418 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6712 (mm) REVERT: B 457 ARG cc_start: 0.5186 (ttt-90) cc_final: 0.4966 (ttt180) REVERT: A 3 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6916 (pp30) REVERT: A 28 THR cc_start: 0.9113 (m) cc_final: 0.8720 (p) REVERT: A 91 THR cc_start: 0.8397 (m) cc_final: 0.8080 (t) REVERT: A 95 TYR cc_start: 0.8541 (m-80) cc_final: 0.8149 (m-80) outliers start: 27 outliers final: 14 residues processed: 124 average time/residue: 0.2001 time to fit residues: 30.6483 Evaluate side-chains 106 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4941 Z= 0.183 Angle : 0.620 11.256 6738 Z= 0.320 Chirality : 0.046 0.172 728 Planarity : 0.005 0.059 878 Dihedral : 5.456 40.434 696 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.81 % Allowed : 5.99 % Favored : 93.20 % Rotamer: Outliers : 5.96 % Allowed : 17.89 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.47 (0.34), residues: 618 helix: -3.17 (0.61), residues: 43 sheet: -0.79 (0.39), residues: 150 loop : -0.79 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.007 0.001 HIS C 505 PHE 0.011 0.001 PHE A 27 TYR 0.015 0.001 TYR A 95 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.478 Fit side-chains REVERT: B 369 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.4737 (p90) REVERT: B 418 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6889 (mm) REVERT: B 457 ARG cc_start: 0.5181 (ttt-90) cc_final: 0.4881 (ttt-90) REVERT: B 519 HIS cc_start: 0.3657 (OUTLIER) cc_final: 0.3367 (p90) REVERT: A 28 THR cc_start: 0.9089 (m) cc_final: 0.8730 (p) REVERT: A 32 TYR cc_start: 0.7616 (m-80) cc_final: 0.7279 (m-10) REVERT: A 35 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7358 (m-40) REVERT: A 95 TYR cc_start: 0.8535 (m-80) cc_final: 0.8269 (m-80) outliers start: 30 outliers final: 19 residues processed: 108 average time/residue: 0.1827 time to fit residues: 25.0074 Evaluate side-chains 107 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4941 Z= 0.253 Angle : 0.645 8.002 6738 Z= 0.333 Chirality : 0.046 0.171 728 Planarity : 0.005 0.061 878 Dihedral : 5.552 39.392 696 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.15 % Favored : 93.04 % Rotamer: Outliers : 7.36 % Allowed : 17.69 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.45 (0.34), residues: 618 helix: -2.73 (0.69), residues: 44 sheet: -0.47 (0.40), residues: 162 loop : -0.97 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 111 HIS 0.006 0.002 HIS C 505 PHE 0.014 0.001 PHE C 377 TYR 0.015 0.002 TYR C 495 ARG 0.008 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 0.592 Fit side-chains REVERT: B 369 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.4894 (p90) REVERT: A 32 TYR cc_start: 0.7895 (m-80) cc_final: 0.7372 (m-10) REVERT: A 35 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7339 (m-40) REVERT: A 95 TYR cc_start: 0.8507 (m-80) cc_final: 0.8304 (m-80) REVERT: D 78 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5713 (ptm-80) outliers start: 37 outliers final: 28 residues processed: 114 average time/residue: 0.1911 time to fit residues: 27.2085 Evaluate side-chains 114 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4941 Z= 0.167 Angle : 0.581 7.187 6738 Z= 0.300 Chirality : 0.045 0.177 728 Planarity : 0.005 0.056 878 Dihedral : 5.133 36.469 696 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.83 % Favored : 93.85 % Rotamer: Outliers : 5.37 % Allowed : 21.67 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.35), residues: 618 helix: -2.65 (0.74), residues: 44 sheet: -0.25 (0.41), residues: 160 loop : -0.84 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.004 0.001 HIS C 505 PHE 0.006 0.001 PHE A 27 TYR 0.014 0.001 TYR A 95 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.4629 (p90) REVERT: C 467 ASP cc_start: 0.6921 (t0) cc_final: 0.6545 (t0) REVERT: A 18 LEU cc_start: 0.7869 (tp) cc_final: 0.7578 (mt) REVERT: A 28 THR cc_start: 0.9116 (m) cc_final: 0.8653 (p) REVERT: A 32 TYR cc_start: 0.7719 (m-80) cc_final: 0.7216 (m-10) outliers start: 27 outliers final: 22 residues processed: 113 average time/residue: 0.1807 time to fit residues: 25.7454 Evaluate side-chains 116 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN B 343 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4941 Z= 0.246 Angle : 0.625 8.364 6738 Z= 0.321 Chirality : 0.045 0.172 728 Planarity : 0.005 0.055 878 Dihedral : 5.305 36.952 696 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.99 % Favored : 93.53 % Rotamer: Outliers : 5.96 % Allowed : 21.47 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.29 (0.34), residues: 618 helix: -2.91 (0.75), residues: 37 sheet: -0.27 (0.41), residues: 162 loop : -0.91 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.003 0.001 HIS B 505 PHE 0.011 0.001 PHE C 377 TYR 0.015 0.002 TYR B 421 ARG 0.004 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.515 Fit side-chains REVERT: B 369 TYR cc_start: 0.5619 (OUTLIER) cc_final: 0.4709 (p90) REVERT: C 467 ASP cc_start: 0.6914 (t0) cc_final: 0.6465 (t0) REVERT: A 32 TYR cc_start: 0.7871 (m-80) cc_final: 0.7395 (m-10) REVERT: A 35 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7245 (m-40) REVERT: D 43 GLN cc_start: 0.8094 (mt0) cc_final: 0.7863 (mt0) REVERT: D 78 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5825 (ptm-80) outliers start: 30 outliers final: 23 residues processed: 104 average time/residue: 0.1889 time to fit residues: 24.6695 Evaluate side-chains 109 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.0570 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 0.0970 chunk 39 optimal weight: 5.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4941 Z= 0.163 Angle : 0.591 6.638 6738 Z= 0.305 Chirality : 0.045 0.180 728 Planarity : 0.005 0.052 878 Dihedral : 5.073 35.701 696 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.34 % Favored : 94.34 % Rotamer: Outliers : 6.16 % Allowed : 21.27 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.22 (0.34), residues: 618 helix: -2.93 (0.68), residues: 43 sheet: -0.16 (0.42), residues: 160 loop : -0.84 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.002 0.001 HIS B 505 PHE 0.008 0.001 PHE C 377 TYR 0.011 0.001 TYR D 37 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.531 Fit side-chains REVERT: B 369 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4685 (p90) REVERT: B 398 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.5423 (p0) REVERT: C 467 ASP cc_start: 0.6875 (t0) cc_final: 0.6410 (t0) REVERT: A 18 LEU cc_start: 0.7834 (tp) cc_final: 0.7602 (mp) REVERT: D 43 GLN cc_start: 0.8080 (mt0) cc_final: 0.7859 (mt0) REVERT: D 78 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5666 (ptm-80) REVERT: D 79 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5729 (mt) REVERT: D 108 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4223 (tp) outliers start: 31 outliers final: 21 residues processed: 107 average time/residue: 0.2044 time to fit residues: 27.1008 Evaluate side-chains 108 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4941 Z= 0.162 Angle : 0.592 6.332 6738 Z= 0.305 Chirality : 0.045 0.158 728 Planarity : 0.005 0.053 878 Dihedral : 4.911 32.723 696 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.02 % Favored : 94.66 % Rotamer: Outliers : 5.37 % Allowed : 22.07 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.15 (0.34), residues: 618 helix: -2.88 (0.70), residues: 43 sheet: -0.13 (0.41), residues: 160 loop : -0.78 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.003 0.001 HIS B 505 PHE 0.008 0.001 PHE C 377 TYR 0.010 0.001 TYR A 80 ARG 0.007 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.672 Fit side-chains REVERT: B 369 TYR cc_start: 0.5619 (OUTLIER) cc_final: 0.4727 (p90) REVERT: B 398 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.5564 (p0) REVERT: B 400 PHE cc_start: 0.5878 (p90) cc_final: 0.5562 (p90) REVERT: C 362 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7885 (t) REVERT: C 467 ASP cc_start: 0.6771 (t0) cc_final: 0.6290 (t0) REVERT: A 32 TYR cc_start: 0.7603 (m-80) cc_final: 0.7112 (m-10) REVERT: A 44 GLU cc_start: 0.7756 (pm20) cc_final: 0.7457 (pm20) REVERT: D 43 GLN cc_start: 0.8026 (mt0) cc_final: 0.7816 (mt0) REVERT: D 78 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5716 (ptm-80) REVERT: D 79 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.5957 (mt) REVERT: D 108 ILE cc_start: 0.4605 (OUTLIER) cc_final: 0.3977 (tp) outliers start: 27 outliers final: 19 residues processed: 102 average time/residue: 0.1889 time to fit residues: 24.7105 Evaluate side-chains 108 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4941 Z= 0.171 Angle : 0.595 6.296 6738 Z= 0.305 Chirality : 0.045 0.166 728 Planarity : 0.005 0.053 878 Dihedral : 4.821 35.290 696 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.85 % Favored : 94.66 % Rotamer: Outliers : 5.96 % Allowed : 21.47 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.12 (0.34), residues: 618 helix: -2.88 (0.70), residues: 43 sheet: -0.09 (0.41), residues: 160 loop : -0.77 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 111 HIS 0.003 0.001 HIS B 505 PHE 0.009 0.001 PHE C 377 TYR 0.010 0.001 TYR A 80 ARG 0.007 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.4748 (p90) REVERT: B 398 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.5612 (p0) REVERT: B 400 PHE cc_start: 0.5789 (p90) cc_final: 0.5420 (p90) REVERT: C 362 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7919 (t) REVERT: C 467 ASP cc_start: 0.6791 (t0) cc_final: 0.6285 (t0) REVERT: A 32 TYR cc_start: 0.7616 (m-80) cc_final: 0.7137 (m-10) REVERT: D 43 GLN cc_start: 0.8032 (mt0) cc_final: 0.7785 (mt0) REVERT: D 78 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5616 (ptm-80) REVERT: D 79 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5966 (mt) REVERT: D 108 ILE cc_start: 0.4425 (OUTLIER) cc_final: 0.3741 (tp) outliers start: 30 outliers final: 24 residues processed: 101 average time/residue: 0.1670 time to fit residues: 21.7251 Evaluate side-chains 111 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4941 Z= 0.190 Angle : 0.596 6.019 6738 Z= 0.307 Chirality : 0.045 0.168 728 Planarity : 0.005 0.053 878 Dihedral : 4.848 34.602 696 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.18 % Favored : 94.34 % Rotamer: Outliers : 5.77 % Allowed : 22.07 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.34), residues: 618 helix: -2.70 (0.69), residues: 43 sheet: 0.04 (0.41), residues: 158 loop : -0.79 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.002 0.001 HIS B 505 PHE 0.011 0.001 PHE C 377 TYR 0.010 0.001 TYR C 473 ARG 0.006 0.001 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.4797 (p90) REVERT: B 398 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.5625 (p0) REVERT: B 400 PHE cc_start: 0.5926 (p90) cc_final: 0.5576 (p90) REVERT: C 467 ASP cc_start: 0.6832 (t0) cc_final: 0.6313 (t0) REVERT: A 32 TYR cc_start: 0.7628 (m-80) cc_final: 0.7184 (m-10) REVERT: D 78 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5514 (ptm-80) REVERT: D 79 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6150 (mt) REVERT: D 108 ILE cc_start: 0.3911 (OUTLIER) cc_final: 0.3201 (tp) outliers start: 29 outliers final: 22 residues processed: 100 average time/residue: 0.1719 time to fit residues: 22.0642 Evaluate side-chains 107 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.172537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129796 restraints weight = 9535.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132357 restraints weight = 5815.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134111 restraints weight = 4244.148| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4941 Z= 0.188 Angle : 0.595 5.991 6738 Z= 0.307 Chirality : 0.045 0.164 728 Planarity : 0.005 0.056 878 Dihedral : 4.846 34.808 696 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.66 % Favored : 93.85 % Rotamer: Outliers : 5.77 % Allowed : 22.47 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.34), residues: 618 helix: -2.68 (0.70), residues: 43 sheet: -0.02 (0.40), residues: 159 loop : -0.84 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 111 HIS 0.002 0.001 HIS A 59 PHE 0.010 0.001 PHE C 377 TYR 0.010 0.001 TYR C 473 ARG 0.006 0.001 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.60 seconds wall clock time: 28 minutes 6.82 seconds (1686.82 seconds total)