Starting phenix.real_space_refine on Mon Mar 18 10:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soi_40658/03_2024/8soi_40658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soi_40658/03_2024/8soi_40658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soi_40658/03_2024/8soi_40658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soi_40658/03_2024/8soi_40658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soi_40658/03_2024/8soi_40658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soi_40658/03_2024/8soi_40658.pdb" } resolution = 4.2 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= 0.032 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 6514 2.51 5 N 1786 2.21 5 O 1863 1.98 5 H 10465 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 573": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20708 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 8222 Classifications: {'peptide': 505} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486} Chain breaks: 1 Chain: "B" Number of atoms: 8393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8393 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 497} Chain breaks: 1 Chain: "C" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3302 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain: "D" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 791 Classifications: {'peptide': 51} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain breaks: 1 Time building chain proxies: 8.39, per 1000 atoms: 0.41 Number of scatterers: 20708 At special positions: 0 Unit cell: (133.35, 150.15, 195.3, 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) S 80 16.00 O 1863 8.00 N 1786 7.00 C 6514 6.00 H 10465 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 379 " distance=2.04 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: 16.91 Conformation dependent library (CDL) restraints added in 2.3 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 75.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.763A pdb=" N VAL A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 23' Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 111 through 180 removed outlier: 3.609A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 336 through 355 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.594A pdb=" N LYS A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 403 removed outlier: 3.863A pdb=" N GLN A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 543 removed outlier: 4.290A pdb=" N ASP A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.566A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.729A pdb=" N VAL B 22 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.737A pdb=" N ASP B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 200 removed outlier: 3.725A pdb=" N GLU B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 336 through 355 Proline residue: B 342 - end of helix Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 364 through 404 removed outlier: 3.643A pdb=" N GLY B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 491 removed outlier: 4.367A pdb=" N LYS B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 543 removed outlier: 3.678A pdb=" N LYS B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.511A pdb=" N SER B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 864 removed outlier: 3.734A pdb=" N ARG C 845 " --> pdb=" O THR C 841 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 859 " --> pdb=" O GLN C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 891 removed outlier: 4.315A pdb=" N ASP C 885 " --> pdb=" O SER C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 923 removed outlier: 4.043A pdb=" N GLY C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 971 removed outlier: 4.165A pdb=" N GLN C 934 " --> pdb=" O SER C 930 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE C 960 " --> pdb=" O ARG C 956 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU C 967 " --> pdb=" O ASP C 963 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 997 Processing helix chain 'C' and resid 1002 through 1021 removed outlier: 3.953A pdb=" N ARG C1006 " --> pdb=" O GLY C1002 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS C1019 " --> pdb=" O GLU C1015 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C1020 " --> pdb=" O GLY C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1044 Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 488 through 514 Proline residue: D 496 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 4.156A pdb=" N LEU A 3 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 4 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU A 73 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 6 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN A 75 " --> pdb=" O PHE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 783 hydrogen bonds defined for protein. 2313 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: 7.36 Time building geometry restraints manager: 17.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10425 1.04 - 1.24: 1339 1.24 - 1.44: 2980 1.44 - 1.64: 6022 1.64 - 1.84: 118 Bond restraints: 20884 Sorted by residual: bond pdb=" N ASP D 462 " pdb=" H1 ASP D 462 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CB LEU B 430 " pdb=" CG LEU B 430 " ideal model delta sigma weight residual 1.530 1.507 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C ILE A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.326 1.342 -0.016 1.44e-02 4.82e+03 1.20e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CG MET B 154 " pdb=" SD MET B 154 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 20879 not shown) Histogram of bond angle deviations from ideal: 73.52 - 85.61: 3 85.61 - 97.71: 0 97.71 - 109.80: 16095 109.80 - 121.89: 18453 121.89 - 133.99: 3299 Bond angle restraints: 37850 Sorted by residual: angle pdb=" CB SER A 176 " pdb=" CA SER A 176 " pdb=" HA SER A 176 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C SER A 176 " pdb=" CA SER A 176 " pdb=" HA SER A 176 " ideal model delta sigma weight residual 109.00 74.77 34.23 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N SER A 176 " pdb=" CA SER A 176 " pdb=" HA SER A 176 " ideal model delta sigma weight residual 110.00 75.90 34.10 3.00e+00 1.11e-01 1.29e+02 angle pdb=" CA GLU B 443 " pdb=" CB GLU B 443 " pdb=" CG GLU B 443 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 8.99e+00 angle pdb=" N GLU B 206 " pdb=" CA GLU B 206 " pdb=" C GLU B 206 " ideal model delta sigma weight residual 112.87 109.61 3.26 1.20e+00 6.94e-01 7.36e+00 ... (remaining 37845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8690 17.84 - 35.67: 746 35.67 - 53.51: 206 53.51 - 71.34: 55 71.34 - 89.18: 16 Dihedral angle restraints: 9713 sinusoidal: 5371 harmonic: 4342 Sorted by residual: dihedral pdb=" CA LEU B 585 " pdb=" C LEU B 585 " pdb=" N GLN B 586 " pdb=" CA GLN B 586 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS B 216 " pdb=" C CYS B 216 " pdb=" N LEU B 217 " pdb=" CA LEU B 217 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual 93.00 55.40 37.60 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 9710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1492 0.067 - 0.134: 110 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 1 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA SER A 176 " pdb=" N SER A 176 " pdb=" C SER A 176 " pdb=" CB SER A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA CYS B 133 " pdb=" N CYS B 133 " pdb=" C CYS B 133 " pdb=" CB CYS B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CG LEU A 365 " pdb=" CB LEU A 365 " pdb=" CD1 LEU A 365 " pdb=" CD2 LEU A 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1603 not shown) Planarity restraints: 3019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 141 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C HIS B 141 " -0.041 2.00e-02 2.50e+03 pdb=" O HIS B 141 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP B 142 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 594 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO B 595 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 595 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 595 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1007 " -0.010 2.00e-02 2.50e+03 8.69e-03 2.26e+00 pdb=" CG TYR C1007 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C1007 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C1007 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C1007 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C1007 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C1007 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C1007 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR C1007 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR C1007 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR C1007 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR C1007 " -0.002 2.00e-02 2.50e+03 ... (remaining 3016 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 721 2.15 - 2.76: 40533 2.76 - 3.38: 60814 3.38 - 3.99: 71886 3.99 - 4.60: 115162 Nonbonded interactions: 289116 Sorted by model distance: nonbonded pdb=" O ALA B 361 " pdb="HH21 ARG B 451 " model vdw 1.539 1.850 nonbonded pdb="HH22 ARG A 535 " pdb=" OD2 ASP B 571 " model vdw 1.540 1.850 nonbonded pdb=" O PHE D 512 " pdb=" H THR D 515 " model vdw 1.566 1.850 nonbonded pdb=" O ARG A 58 " pdb=" HG1 THR A 61 " model vdw 1.577 1.850 nonbonded pdb=" OD2 ASP A 571 " pdb="HH22 ARG B 535 " model vdw 1.579 1.850 ... (remaining 289111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 134 through 378 or (resid 379 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 380 through 597)) selection = (chain 'B' and (resid 1 through 208 or resid 304 through 460 or (resid 461 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1 or name HE2)) or resid 462 through 597)) } 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: 2.290 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: 0.320 Extract box with map and model: 10.610 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 65.220 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 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 : 0.003 0.036 10419 Z= 0.208 Angle : 0.599 7.631 14041 Z= 0.331 Chirality : 0.036 0.335 1606 Planarity : 0.003 0.043 1790 Dihedral : 15.468 89.178 3965 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 13.32 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.61 (0.24), residues: 1262 helix: 1.75 (0.17), residues: 878 sheet: -0.21 (0.88), residues: 28 loop : -0.50 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 150 HIS 0.004 0.001 HIS B 211 PHE 0.017 0.002 PHE B 74 TYR 0.025 0.002 TYR C1007 ARG 0.003 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7533 (tp30) cc_final: 0.6709 (tp30) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.5440 time to fit residues: 115.1163 Evaluate side-chains 152 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10419 Z= 0.258 Angle : 0.580 6.170 14041 Z= 0.324 Chirality : 0.037 0.344 1606 Planarity : 0.004 0.075 1790 Dihedral : 5.078 26.789 1372 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.46 (0.24), residues: 1262 helix: 1.76 (0.17), residues: 871 sheet: -0.81 (0.90), residues: 30 loop : -0.83 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 516 HIS 0.011 0.001 HIS B 42 PHE 0.020 0.002 PHE A 393 TYR 0.018 0.002 TYR D 467 ARG 0.010 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7415 (t80) cc_final: 0.7108 (t80) REVERT: A 435 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8866 (tm-30) REVERT: A 459 MET cc_start: 0.5898 (ttp) cc_final: 0.5599 (ttp) REVERT: A 508 MET cc_start: 0.7935 (ttp) cc_final: 0.7631 (mtp) REVERT: B 140 VAL cc_start: 0.9091 (t) cc_final: 0.8777 (t) REVERT: B 154 MET cc_start: 0.7663 (mtt) cc_final: 0.7272 (mtt) REVERT: B 432 ASP cc_start: 0.8581 (m-30) cc_final: 0.8304 (m-30) REVERT: C 1033 CYS cc_start: 0.8363 (m) cc_final: 0.7958 (m) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.5059 time to fit residues: 129.5650 Evaluate side-chains 151 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10419 Z= 0.206 Angle : 0.548 9.149 14041 Z= 0.304 Chirality : 0.035 0.340 1606 Planarity : 0.003 0.041 1790 Dihedral : 5.017 26.019 1372 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.61 (0.24), residues: 1262 helix: 1.89 (0.17), residues: 875 sheet: -0.42 (0.87), residues: 33 loop : -0.88 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 516 HIS 0.007 0.001 HIS A 147 PHE 0.021 0.002 PHE A 393 TYR 0.014 0.001 TYR B 370 ARG 0.003 0.000 ARG C1040 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.7802 (mt0) cc_final: 0.7345 (mt0) REVERT: A 435 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8837 (tm-30) REVERT: A 459 MET cc_start: 0.5931 (ttp) cc_final: 0.5678 (ttp) REVERT: A 508 MET cc_start: 0.7910 (ttp) cc_final: 0.7488 (mtp) REVERT: A 525 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7330 (pttm) REVERT: B 42 HIS cc_start: 0.6189 (m-70) cc_final: 0.5963 (m-70) REVERT: B 140 VAL cc_start: 0.9055 (t) cc_final: 0.8775 (t) REVERT: B 175 TYR cc_start: 0.7369 (m-80) cc_final: 0.6901 (m-80) REVERT: B 432 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: C 1033 CYS cc_start: 0.8431 (m) cc_final: 0.8002 (t) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.5330 time to fit residues: 133.7652 Evaluate side-chains 151 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10419 Z= 0.317 Angle : 0.605 9.209 14041 Z= 0.340 Chirality : 0.037 0.355 1606 Planarity : 0.004 0.044 1790 Dihedral : 5.144 28.210 1372 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.36 (0.24), residues: 1262 helix: 1.69 (0.17), residues: 886 sheet: -1.69 (0.94), residues: 32 loop : -0.89 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 516 HIS 0.006 0.001 HIS A 141 PHE 0.018 0.002 PHE A 393 TYR 0.017 0.002 TYR B 175 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8705 (tp) cc_final: 0.8468 (tp) REVERT: A 148 GLN cc_start: 0.7811 (mt0) cc_final: 0.7347 (mt0) REVERT: A 435 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8851 (tm-30) REVERT: A 459 MET cc_start: 0.6091 (ttp) cc_final: 0.5810 (ttp) REVERT: A 508 MET cc_start: 0.7954 (ttp) cc_final: 0.7595 (mtp) REVERT: B 140 VAL cc_start: 0.9168 (t) cc_final: 0.8888 (t) REVERT: B 162 ASN cc_start: 0.8893 (m110) cc_final: 0.8639 (m110) REVERT: B 432 ASP cc_start: 0.8597 (m-30) cc_final: 0.8314 (m-30) REVERT: C 1033 CYS cc_start: 0.8270 (m) cc_final: 0.7924 (m) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.5183 time to fit residues: 129.0596 Evaluate side-chains 157 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10419 Z= 0.340 Angle : 0.613 8.516 14041 Z= 0.345 Chirality : 0.037 0.357 1606 Planarity : 0.004 0.050 1790 Dihedral : 5.222 29.656 1372 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.24), residues: 1262 helix: 1.68 (0.17), residues: 878 sheet: -1.88 (0.96), residues: 32 loop : -1.11 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 516 HIS 0.007 0.001 HIS A 141 PHE 0.026 0.002 PHE A 542 TYR 0.019 0.002 TYR B 175 ARG 0.003 0.000 ARG C 956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8671 (tp) cc_final: 0.8375 (tp) REVERT: A 148 GLN cc_start: 0.7766 (mt0) cc_final: 0.7284 (mt0) REVERT: A 322 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7188 (tp30) REVERT: A 435 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8855 (tm-30) REVERT: A 459 MET cc_start: 0.6151 (ttp) cc_final: 0.5897 (ttp) REVERT: A 508 MET cc_start: 0.7968 (ttp) cc_final: 0.7572 (mtp) REVERT: B 140 VAL cc_start: 0.9188 (t) cc_final: 0.8927 (t) REVERT: B 158 GLU cc_start: 0.8672 (pp20) cc_final: 0.8299 (pp20) REVERT: C 880 GLU cc_start: 0.6649 (tt0) cc_final: 0.6346 (tt0) REVERT: C 1033 CYS cc_start: 0.8341 (m) cc_final: 0.8130 (t) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.5526 time to fit residues: 134.0977 Evaluate side-chains 157 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10419 Z= 0.224 Angle : 0.557 8.668 14041 Z= 0.309 Chirality : 0.036 0.344 1606 Planarity : 0.003 0.044 1790 Dihedral : 5.090 27.819 1372 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.43 (0.24), residues: 1262 helix: 1.81 (0.17), residues: 883 sheet: -1.85 (0.96), residues: 32 loop : -1.02 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 516 HIS 0.008 0.001 HIS A 147 PHE 0.017 0.002 PHE A 542 TYR 0.018 0.002 TYR A 36 ARG 0.003 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8623 (tp) cc_final: 0.8326 (tp) REVERT: A 148 GLN cc_start: 0.7803 (mt0) cc_final: 0.7346 (mt0) REVERT: A 322 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7199 (tp30) REVERT: A 435 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 459 MET cc_start: 0.6131 (ttp) cc_final: 0.5703 (ttp) REVERT: A 508 MET cc_start: 0.7932 (ttp) cc_final: 0.7525 (mtp) REVERT: A 525 LYS cc_start: 0.7857 (tttm) cc_final: 0.7312 (pttt) REVERT: B 140 VAL cc_start: 0.9109 (t) cc_final: 0.8803 (t) REVERT: B 162 ASN cc_start: 0.8938 (m110) cc_final: 0.8730 (m110) REVERT: B 432 ASP cc_start: 0.8617 (m-30) cc_final: 0.8289 (m-30) REVERT: C 880 GLU cc_start: 0.6603 (tt0) cc_final: 0.6281 (tt0) REVERT: C 1033 CYS cc_start: 0.8320 (m) cc_final: 0.7898 (m) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.5193 time to fit residues: 132.5924 Evaluate side-chains 158 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 419 GLN B 384 ASN D 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10419 Z= 0.207 Angle : 0.532 7.204 14041 Z= 0.295 Chirality : 0.035 0.341 1606 Planarity : 0.003 0.050 1790 Dihedral : 5.039 31.836 1372 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 0.09 % Allowed : 0.79 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.57 (0.24), residues: 1262 helix: 1.92 (0.17), residues: 880 sheet: -1.75 (0.96), residues: 32 loop : -0.97 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 516 HIS 0.009 0.001 HIS B 427 PHE 0.024 0.002 PHE D 466 TYR 0.015 0.001 TYR A 36 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8617 (tp) cc_final: 0.8328 (tp) REVERT: A 148 GLN cc_start: 0.7719 (mt0) cc_final: 0.7238 (mt0) REVERT: A 322 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7203 (tp30) REVERT: A 435 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8863 (tm-30) REVERT: A 459 MET cc_start: 0.6120 (ttp) cc_final: 0.5829 (ttp) REVERT: A 508 MET cc_start: 0.7859 (ttp) cc_final: 0.7368 (mtp) REVERT: B 140 VAL cc_start: 0.9119 (t) cc_final: 0.8770 (t) REVERT: B 162 ASN cc_start: 0.8937 (m110) cc_final: 0.8728 (m110) REVERT: B 432 ASP cc_start: 0.8617 (m-30) cc_final: 0.8295 (m-30) REVERT: C 880 GLU cc_start: 0.6612 (tt0) cc_final: 0.6249 (tt0) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.5166 time to fit residues: 130.5790 Evaluate side-chains 161 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 419 GLN D 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10419 Z= 0.212 Angle : 0.532 6.262 14041 Z= 0.293 Chirality : 0.035 0.343 1606 Planarity : 0.003 0.045 1790 Dihedral : 4.939 25.797 1372 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.65 (0.24), residues: 1262 helix: 1.98 (0.17), residues: 880 sheet: -1.65 (0.98), residues: 32 loop : -0.94 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 516 HIS 0.008 0.001 HIS B 427 PHE 0.014 0.002 PHE A 542 TYR 0.014 0.001 TYR B 370 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8633 (tp) cc_final: 0.8303 (tp) REVERT: A 148 GLN cc_start: 0.7731 (mt0) cc_final: 0.7245 (mt0) REVERT: A 322 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7195 (tp30) REVERT: A 435 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 457 PHE cc_start: 0.6016 (t80) cc_final: 0.5757 (t80) REVERT: A 459 MET cc_start: 0.6265 (ttp) cc_final: 0.5978 (ttp) REVERT: A 508 MET cc_start: 0.7822 (ttp) cc_final: 0.7348 (mtp) REVERT: B 140 VAL cc_start: 0.9124 (t) cc_final: 0.8780 (t) REVERT: B 162 ASN cc_start: 0.8942 (m110) cc_final: 0.8731 (m110) REVERT: B 432 ASP cc_start: 0.8616 (m-30) cc_final: 0.8298 (m-30) REVERT: C 880 GLU cc_start: 0.6592 (tt0) cc_final: 0.6218 (tt0) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.5313 time to fit residues: 136.1610 Evaluate side-chains 163 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 419 GLN D 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10419 Z= 0.226 Angle : 0.536 5.068 14041 Z= 0.298 Chirality : 0.035 0.345 1606 Planarity : 0.004 0.064 1790 Dihedral : 4.908 25.671 1372 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.64 (0.24), residues: 1262 helix: 1.99 (0.17), residues: 880 sheet: -1.65 (0.98), residues: 32 loop : -0.99 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 516 HIS 0.007 0.001 HIS A 147 PHE 0.020 0.002 PHE D 466 TYR 0.013 0.001 TYR B 370 ARG 0.002 0.000 ARG C 892 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.7720 (mt0) cc_final: 0.7289 (mt0) REVERT: A 435 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 457 PHE cc_start: 0.5957 (t80) cc_final: 0.5657 (t80) REVERT: A 459 MET cc_start: 0.6276 (ttp) cc_final: 0.5984 (ttp) REVERT: A 508 MET cc_start: 0.7794 (ttp) cc_final: 0.7294 (mtp) REVERT: B 140 VAL cc_start: 0.9132 (t) cc_final: 0.8792 (t) REVERT: B 162 ASN cc_start: 0.8945 (m110) cc_final: 0.8736 (m110) REVERT: B 432 ASP cc_start: 0.8599 (m-30) cc_final: 0.8281 (m-30) REVERT: B 459 MET cc_start: -0.0382 (ttt) cc_final: -0.0585 (ttt) REVERT: C 880 GLU cc_start: 0.6535 (tt0) cc_final: 0.6194 (tt0) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.5119 time to fit residues: 129.4118 Evaluate side-chains 161 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 106 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10419 Z= 0.192 Angle : 0.523 7.328 14041 Z= 0.287 Chirality : 0.035 0.341 1606 Planarity : 0.003 0.045 1790 Dihedral : 4.832 24.601 1372 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.49 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1262 helix: 2.08 (0.17), residues: 880 sheet: -1.64 (0.97), residues: 32 loop : -0.93 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 516 HIS 0.008 0.001 HIS A 147 PHE 0.014 0.002 PHE D 466 TYR 0.013 0.001 TYR B 370 ARG 0.005 0.000 ARG B 506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.7770 (mt0) cc_final: 0.7422 (mt0) REVERT: A 435 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8846 (tm-30) REVERT: A 457 PHE cc_start: 0.5944 (t80) cc_final: 0.5728 (t80) REVERT: A 459 MET cc_start: 0.6334 (ttp) cc_final: 0.6077 (ttp) REVERT: A 508 MET cc_start: 0.7768 (ttp) cc_final: 0.7293 (mtp) REVERT: B 140 VAL cc_start: 0.9115 (t) cc_final: 0.8762 (t) REVERT: B 162 ASN cc_start: 0.8943 (m110) cc_final: 0.8729 (m110) REVERT: B 432 ASP cc_start: 0.8611 (m-30) cc_final: 0.8274 (m-30) REVERT: C 880 GLU cc_start: 0.6577 (tt0) cc_final: 0.6186 (tt0) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.5088 time to fit residues: 126.4401 Evaluate side-chains 154 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 8.9990 chunk 92 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.173712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151869 restraints weight = 79678.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.155667 restraints weight = 41820.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.156825 restraints weight = 27387.903| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10419 Z= 0.190 Angle : 0.517 7.899 14041 Z= 0.283 Chirality : 0.035 0.341 1606 Planarity : 0.003 0.045 1790 Dihedral : 4.764 23.741 1372 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.28 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.87 (0.24), residues: 1262 helix: 2.15 (0.17), residues: 879 sheet: -1.52 (0.95), residues: 32 loop : -0.88 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 516 HIS 0.008 0.001 HIS A 147 PHE 0.013 0.001 PHE D 466 TYR 0.013 0.001 TYR B 370 ARG 0.004 0.000 ARG B 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4409.32 seconds wall clock time: 79 minutes 3.30 seconds (4743.30 seconds total)