Starting phenix.real_space_refine on Sat Jan 20 01:30:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e87_31011/01_2024/7e87_31011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e87_31011/01_2024/7e87_31011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e87_31011/01_2024/7e87_31011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e87_31011/01_2024/7e87_31011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e87_31011/01_2024/7e87_31011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e87_31011/01_2024/7e87_31011.pdb" } resolution = 3.4 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= 0.000 sd= 0.002 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 70 5.16 5 C 8642 2.51 5 N 2242 2.21 5 O 2350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13304 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "I" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "D" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "E" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 6.97, per 1000 atoms: 0.52 Number of scatterers: 13304 At special positions: 0 Unit cell: (109, 111, 129, 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 70 16.00 O 2350 8.00 N 2242 7.00 C 8642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 4 sheets defined 73.0% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.718A pdb=" N PHE B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.573A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.618A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.976A pdb=" N ARG B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 228 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.542A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 434 removed outlier: 3.990A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.661A pdb=" N PHE A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.603A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.508A pdb=" N ARG A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.690A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 228 through 250 removed outlier: 4.462A pdb=" N ILE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.709A pdb=" N PHE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.978A pdb=" N ARG A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 434 Processing helix chain 'J' and resid 32 through 56 removed outlier: 3.509A pdb=" N ILE J 36 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.717A pdb=" N PHE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.573A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.618A pdb=" N PHE C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.976A pdb=" N ARG C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 228 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.542A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 434 removed outlier: 3.989A pdb=" N ASP C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS C 421 " --> pdb=" O GLN C 417 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 88 through 101 removed outlier: 3.661A pdb=" N PHE D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.603A pdb=" N ILE D 128 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 129 " --> pdb=" O PRO D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 129' Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.506A pdb=" N ARG D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.690A pdb=" N ASN D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 228 through 250 removed outlier: 4.463A pdb=" N ILE D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.708A pdb=" N PHE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.978A pdb=" N ARG D 299 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 434 Processing helix chain 'E' and resid 32 through 56 removed outlier: 3.509A pdb=" N ILE E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.803A pdb=" N THR A 54 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 43 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.802A pdb=" N THR D 54 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 43 " --> pdb=" O THR D 54 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2532 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: 3.99 Time building geometry restraints manager: 6.06 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: 2917 1.33 - 1.45: 3108 1.45 - 1.57: 7483 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 13612 Sorted by residual: bond pdb=" C LEU C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.332 1.354 -0.022 8.20e-03 1.49e+04 7.08e+00 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.332 1.353 -0.021 8.20e-03 1.49e+04 6.60e+00 bond pdb=" C THR I 56 " pdb=" N PRO I 57 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.68e+00 bond pdb=" C THR F 56 " pdb=" N PRO F 57 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.68e+00 bond pdb=" CG LEU C 271 " pdb=" CD1 LEU C 271 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 13607 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.76: 237 105.76 - 112.84: 7160 112.84 - 119.91: 4799 119.91 - 126.98: 6125 126.98 - 134.05: 133 Bond angle restraints: 18454 Sorted by residual: angle pdb=" N GLN A 417 " pdb=" CA GLN A 417 " pdb=" CB GLN A 417 " ideal model delta sigma weight residual 110.28 116.69 -6.41 1.55e+00 4.16e-01 1.71e+01 angle pdb=" N GLN D 417 " pdb=" CA GLN D 417 " pdb=" CB GLN D 417 " ideal model delta sigma weight residual 110.28 116.65 -6.37 1.55e+00 4.16e-01 1.69e+01 angle pdb=" N ILE B 112 " pdb=" CA ILE B 112 " pdb=" C ILE B 112 " ideal model delta sigma weight residual 112.12 109.32 2.80 8.40e-01 1.42e+00 1.11e+01 angle pdb=" N ILE C 112 " pdb=" CA ILE C 112 " pdb=" C ILE C 112 " ideal model delta sigma weight residual 112.12 109.36 2.76 8.40e-01 1.42e+00 1.08e+01 angle pdb=" N LEU A 271 " pdb=" CA LEU A 271 " pdb=" C LEU A 271 " ideal model delta sigma weight residual 109.81 116.98 -7.17 2.21e+00 2.05e-01 1.05e+01 ... (remaining 18449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 7091 16.05 - 32.10: 749 32.10 - 48.15: 168 48.15 - 64.20: 26 64.20 - 80.25: 8 Dihedral angle restraints: 8042 sinusoidal: 3154 harmonic: 4888 Sorted by residual: dihedral pdb=" CA VAL D 297 " pdb=" C VAL D 297 " pdb=" N PHE D 298 " pdb=" CA PHE D 298 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL A 297 " pdb=" C VAL A 297 " pdb=" N PHE A 298 " pdb=" CA PHE A 298 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO B 89 " pdb=" C PRO B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1448 0.040 - 0.080: 511 0.080 - 0.119: 138 0.119 - 0.159: 11 0.159 - 0.199: 8 Chirality restraints: 2116 Sorted by residual: chirality pdb=" CA LEU C 271 " pdb=" N LEU C 271 " pdb=" C LEU C 271 " pdb=" CB LEU C 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 2113 not shown) Planarity restraints: 2306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 235 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ALA C 235 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA C 235 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS C 236 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 235 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C ALA B 235 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 235 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS B 236 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 238 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C MET C 238 " -0.027 2.00e-02 2.50e+03 pdb=" O MET C 238 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 239 " 0.009 2.00e-02 2.50e+03 ... (remaining 2303 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 268 2.67 - 3.23: 14220 3.23 - 3.78: 21300 3.78 - 4.34: 27696 4.34 - 4.90: 44582 Nonbonded interactions: 108066 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" OE1 GLU A 71 " model vdw 2.111 2.440 nonbonded pdb=" OG SER D 69 " pdb=" OE1 GLU D 71 " model vdw 2.112 2.440 nonbonded pdb=" OD1 ASN C 97 " pdb=" NH1 ARG C 100 " model vdw 2.150 2.520 nonbonded pdb=" OD1 ASN B 97 " pdb=" NH1 ARG B 100 " model vdw 2.150 2.520 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.174 2.440 ... (remaining 108061 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 40 through 158 or resid 167 through 436)) selection = (chain 'B' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'C' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'D' and (resid 40 through 158 or resid 167 through 436)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.870 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.830 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.044 13612 Z= 0.222 Angle : 0.648 8.571 18454 Z= 0.345 Chirality : 0.044 0.199 2116 Planarity : 0.005 0.039 2306 Dihedral : 13.861 80.250 4882 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1632 helix: 0.84 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 31 HIS 0.004 0.001 HIS D 306 PHE 0.017 0.002 PHE D 187 TYR 0.019 0.001 TYR A 83 ARG 0.008 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 1.583 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: B 97 ASN cc_start: 0.8210 (t0) cc_final: 0.7790 (t0) REVERT: B 98 PHE cc_start: 0.8324 (t80) cc_final: 0.7862 (t80) REVERT: B 110 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 224 ARG cc_start: 0.4502 (pmt170) cc_final: 0.4296 (ptm160) REVERT: B 238 MET cc_start: 0.8048 (mmp) cc_final: 0.7808 (mmp) REVERT: B 308 GLN cc_start: 0.7033 (pm20) cc_final: 0.6823 (pm20) REVERT: B 315 TYR cc_start: 0.7165 (m-10) cc_final: 0.6844 (m-10) REVERT: B 318 LYS cc_start: 0.7209 (mptt) cc_final: 0.6870 (mptt) REVERT: B 418 ARG cc_start: 0.6524 (ptm-80) cc_final: 0.6301 (ptt90) REVERT: A 53 GLN cc_start: 0.7820 (mp10) cc_final: 0.7582 (mp10) REVERT: A 66 LEU cc_start: 0.7587 (tt) cc_final: 0.7168 (tt) REVERT: A 71 GLU cc_start: 0.7421 (mp0) cc_final: 0.7108 (mp0) REVERT: A 81 GLN cc_start: 0.6461 (mp10) cc_final: 0.5839 (mp10) REVERT: A 136 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 138 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7851 (mmmm) REVERT: A 149 GLN cc_start: 0.6885 (pp30) cc_final: 0.6603 (pp30) REVERT: A 170 ARG cc_start: 0.6707 (tpp-160) cc_final: 0.5860 (tpt170) REVERT: A 172 TRP cc_start: 0.7246 (t60) cc_final: 0.6794 (t60) REVERT: A 176 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 312 ILE cc_start: 0.8604 (mt) cc_final: 0.8326 (mt) REVERT: C 97 ASN cc_start: 0.8216 (t0) cc_final: 0.7791 (t0) REVERT: C 98 PHE cc_start: 0.8331 (t80) cc_final: 0.7870 (t80) REVERT: C 110 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 224 ARG cc_start: 0.4517 (pmt170) cc_final: 0.4299 (ptm160) REVERT: C 238 MET cc_start: 0.8047 (mmp) cc_final: 0.7806 (mmp) REVERT: C 308 GLN cc_start: 0.7034 (pm20) cc_final: 0.6825 (pm20) REVERT: C 315 TYR cc_start: 0.7102 (m-10) cc_final: 0.6797 (m-10) REVERT: C 318 LYS cc_start: 0.7210 (mptt) cc_final: 0.6873 (mptt) REVERT: C 418 ARG cc_start: 0.6519 (ptm-80) cc_final: 0.6298 (ptt90) REVERT: D 53 GLN cc_start: 0.7817 (mp10) cc_final: 0.7578 (mp10) REVERT: D 66 LEU cc_start: 0.7581 (tt) cc_final: 0.7162 (tt) REVERT: D 71 GLU cc_start: 0.7426 (mp0) cc_final: 0.7115 (mp0) REVERT: D 81 GLN cc_start: 0.6462 (mp10) cc_final: 0.5735 (mp10) REVERT: D 136 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 138 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7846 (mmmm) REVERT: D 149 GLN cc_start: 0.6883 (pp30) cc_final: 0.6602 (pp30) REVERT: D 170 ARG cc_start: 0.6706 (tpp-160) cc_final: 0.5857 (tpt170) REVERT: D 172 TRP cc_start: 0.7246 (t60) cc_final: 0.6749 (t60) REVERT: D 176 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 312 ILE cc_start: 0.8600 (mt) cc_final: 0.8316 (mt) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.2826 time to fit residues: 163.7840 Evaluate side-chains 273 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 77 HIS ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN A 82 GLN ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 202 ASN C 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13612 Z= 0.380 Angle : 0.721 8.865 18454 Z= 0.382 Chirality : 0.046 0.192 2116 Planarity : 0.006 0.052 2306 Dihedral : 4.377 17.749 1852 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.30 % Allowed : 13.48 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1632 helix: 0.87 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 362 HIS 0.010 0.002 HIS C 306 PHE 0.029 0.003 PHE D 194 TYR 0.023 0.002 TYR C 188 ARG 0.006 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7418 (mm110) cc_final: 0.6820 (mm-40) REVERT: B 82 GLN cc_start: 0.7816 (mt0) cc_final: 0.7599 (mt0) REVERT: B 97 ASN cc_start: 0.8021 (t0) cc_final: 0.7541 (t0) REVERT: B 98 PHE cc_start: 0.8445 (t80) cc_final: 0.7926 (t80) REVERT: B 318 LYS cc_start: 0.7206 (mptt) cc_final: 0.6991 (mptt) REVERT: A 66 LEU cc_start: 0.7594 (tt) cc_final: 0.7076 (tt) REVERT: A 71 GLU cc_start: 0.7556 (mp0) cc_final: 0.7163 (mp0) REVERT: A 81 GLN cc_start: 0.6406 (mp10) cc_final: 0.5755 (mp10) REVERT: A 82 GLN cc_start: 0.6653 (mm-40) cc_final: 0.6265 (mm110) REVERT: A 138 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7772 (mmmm) REVERT: A 170 ARG cc_start: 0.6361 (tpp-160) cc_final: 0.6061 (tpt170) REVERT: A 172 TRP cc_start: 0.6907 (t60) cc_final: 0.6575 (t60) REVERT: A 176 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7554 (tm-30) REVERT: C 53 GLN cc_start: 0.7406 (mm110) cc_final: 0.6811 (mm-40) REVERT: C 97 ASN cc_start: 0.8018 (t0) cc_final: 0.7537 (t0) REVERT: C 98 PHE cc_start: 0.8449 (t80) cc_final: 0.7933 (t80) REVERT: C 318 LYS cc_start: 0.7209 (mptt) cc_final: 0.6996 (mptt) REVERT: D 66 LEU cc_start: 0.7580 (tt) cc_final: 0.7067 (tt) REVERT: D 71 GLU cc_start: 0.7556 (mp0) cc_final: 0.7155 (mp0) REVERT: D 81 GLN cc_start: 0.6450 (mp10) cc_final: 0.5886 (mp10) REVERT: D 138 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7766 (mmmm) REVERT: D 170 ARG cc_start: 0.6355 (tpp-160) cc_final: 0.6055 (tpt170) REVERT: D 172 TRP cc_start: 0.6909 (t60) cc_final: 0.6578 (t60) REVERT: D 176 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 33 outliers final: 18 residues processed: 297 average time/residue: 0.2466 time to fit residues: 105.4269 Evaluate side-chains 242 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 105 HIS B 202 ASN B 408 ASN A 414 HIS C 46 ASN C 105 HIS C 408 ASN D 82 GLN D 414 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 13612 Z= 0.492 Angle : 0.778 8.583 18454 Z= 0.410 Chirality : 0.049 0.199 2116 Planarity : 0.006 0.056 2306 Dihedral : 4.682 19.773 1852 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.84 % Allowed : 17.53 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1632 helix: 0.54 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -2.43 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 362 HIS 0.012 0.003 HIS B 306 PHE 0.033 0.003 PHE D 194 TYR 0.026 0.003 TYR C 188 ARG 0.006 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 234 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7353 (mm110) cc_final: 0.6712 (mm-40) REVERT: B 175 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6509 (t80) REVERT: B 318 LYS cc_start: 0.7281 (mptt) cc_final: 0.7056 (mptt) REVERT: A 71 GLU cc_start: 0.7510 (mp0) cc_final: 0.7139 (mp0) REVERT: A 81 GLN cc_start: 0.6791 (mp10) cc_final: 0.6208 (mp10) REVERT: A 92 PHE cc_start: 0.8810 (t80) cc_final: 0.8564 (t80) REVERT: A 170 ARG cc_start: 0.6303 (tpp-160) cc_final: 0.5952 (tpt170) REVERT: A 176 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7679 (tm-30) REVERT: J 41 ILE cc_start: 0.8681 (mt) cc_final: 0.8442 (tt) REVERT: C 53 GLN cc_start: 0.7498 (mm110) cc_final: 0.6879 (mm-40) REVERT: C 97 ASN cc_start: 0.7991 (t0) cc_final: 0.7686 (t0) REVERT: C 175 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6486 (t80) REVERT: C 318 LYS cc_start: 0.7284 (mptt) cc_final: 0.7062 (mptt) REVERT: D 71 GLU cc_start: 0.7511 (mp0) cc_final: 0.7136 (mp0) REVERT: D 81 GLN cc_start: 0.6712 (mp10) cc_final: 0.6195 (mp10) REVERT: D 92 PHE cc_start: 0.8809 (t80) cc_final: 0.8565 (t80) REVERT: D 170 ARG cc_start: 0.6300 (tpp-160) cc_final: 0.5948 (tpt170) REVERT: D 176 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7673 (tm-30) REVERT: D 238 MET cc_start: 0.6471 (mtp) cc_final: 0.6154 (mtp) REVERT: E 41 ILE cc_start: 0.8689 (mt) cc_final: 0.8449 (tt) outliers start: 55 outliers final: 42 residues processed: 274 average time/residue: 0.2403 time to fit residues: 97.6904 Evaluate side-chains 257 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 213 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS C 46 ASN C 408 ASN D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13612 Z= 0.213 Angle : 0.616 8.427 18454 Z= 0.323 Chirality : 0.043 0.164 2116 Planarity : 0.005 0.053 2306 Dihedral : 4.198 18.096 1852 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.86 % Allowed : 20.25 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1632 helix: 0.86 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -2.32 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 172 HIS 0.004 0.001 HIS B 105 PHE 0.020 0.002 PHE A 194 TYR 0.018 0.001 TYR C 188 ARG 0.004 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7350 (mm110) cc_final: 0.6747 (mm-40) REVERT: B 97 ASN cc_start: 0.7819 (t0) cc_final: 0.7569 (t0) REVERT: B 98 PHE cc_start: 0.8478 (t80) cc_final: 0.8245 (t80) REVERT: B 138 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8027 (mmtm) REVERT: B 342 MET cc_start: 0.8905 (tpp) cc_final: 0.8581 (mmp) REVERT: B 346 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 392 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 418 ARG cc_start: 0.6541 (ptm-80) cc_final: 0.6036 (ttp80) REVERT: A 66 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7104 (tt) REVERT: A 71 GLU cc_start: 0.7444 (mp0) cc_final: 0.6995 (mp0) REVERT: A 81 GLN cc_start: 0.6541 (mp10) cc_final: 0.6054 (mp10) REVERT: A 136 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 170 ARG cc_start: 0.6366 (tpp-160) cc_final: 0.5982 (tpt170) REVERT: A 176 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 53 GLN cc_start: 0.7312 (mm110) cc_final: 0.6692 (mm-40) REVERT: C 97 ASN cc_start: 0.7815 (t0) cc_final: 0.7578 (t0) REVERT: C 98 PHE cc_start: 0.8476 (t80) cc_final: 0.8246 (t80) REVERT: C 138 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8027 (mmtm) REVERT: C 342 MET cc_start: 0.8909 (tpp) cc_final: 0.8585 (mmp) REVERT: C 346 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 418 ARG cc_start: 0.6537 (ptm-80) cc_final: 0.6035 (ttp80) REVERT: D 66 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7085 (tt) REVERT: D 71 GLU cc_start: 0.7443 (mp0) cc_final: 0.7023 (mp0) REVERT: D 81 GLN cc_start: 0.6569 (mp10) cc_final: 0.6070 (mp10) REVERT: D 136 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 170 ARG cc_start: 0.6363 (tpp-160) cc_final: 0.5978 (tpt170) REVERT: D 176 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 312 ILE cc_start: 0.8452 (mt) cc_final: 0.8252 (mt) outliers start: 41 outliers final: 24 residues processed: 289 average time/residue: 0.2415 time to fit residues: 101.4377 Evaluate side-chains 251 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 0.0970 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 408 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 408 ASN D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13612 Z= 0.195 Angle : 0.602 8.509 18454 Z= 0.314 Chirality : 0.042 0.194 2116 Planarity : 0.004 0.051 2306 Dihedral : 4.023 17.446 1852 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.56 % Allowed : 21.09 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1632 helix: 1.06 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.26 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 172 HIS 0.004 0.001 HIS A 306 PHE 0.024 0.002 PHE A 194 TYR 0.016 0.001 TYR B 188 ARG 0.006 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7434 (mm110) cc_final: 0.6798 (mm-40) REVERT: B 90 ASP cc_start: 0.7388 (m-30) cc_final: 0.6606 (t0) REVERT: B 97 ASN cc_start: 0.7789 (t0) cc_final: 0.7532 (t0) REVERT: B 98 PHE cc_start: 0.8450 (t80) cc_final: 0.8210 (t80) REVERT: B 175 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6493 (t80) REVERT: B 346 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 392 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 418 ARG cc_start: 0.6511 (ptm-80) cc_final: 0.6080 (ttp80) REVERT: A 66 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7049 (tt) REVERT: A 71 GLU cc_start: 0.7512 (mp0) cc_final: 0.7102 (mp0) REVERT: A 81 GLN cc_start: 0.6430 (mp10) cc_final: 0.5988 (mp10) REVERT: A 136 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 170 ARG cc_start: 0.6367 (tpp-160) cc_final: 0.5996 (tpt170) REVERT: A 176 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7584 (tm-30) REVERT: J 41 ILE cc_start: 0.8590 (mt) cc_final: 0.8341 (tt) REVERT: C 53 GLN cc_start: 0.7399 (mm110) cc_final: 0.6751 (mm-40) REVERT: C 90 ASP cc_start: 0.7394 (m-30) cc_final: 0.6608 (t0) REVERT: C 97 ASN cc_start: 0.7755 (t0) cc_final: 0.7519 (t0) REVERT: C 98 PHE cc_start: 0.8413 (t80) cc_final: 0.8181 (t80) REVERT: C 175 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6471 (t80) REVERT: C 346 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7420 (mm-30) REVERT: C 392 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8331 (mt) REVERT: C 418 ARG cc_start: 0.6508 (ptm-80) cc_final: 0.6083 (ttp80) REVERT: D 66 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7041 (tt) REVERT: D 71 GLU cc_start: 0.7517 (mp0) cc_final: 0.7100 (mp0) REVERT: D 81 GLN cc_start: 0.6467 (mp10) cc_final: 0.6019 (mp10) REVERT: D 90 ASP cc_start: 0.8361 (m-30) cc_final: 0.8161 (m-30) REVERT: D 136 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7685 (tm-30) REVERT: D 170 ARG cc_start: 0.6365 (tpp-160) cc_final: 0.5992 (tpt170) REVERT: D 176 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 312 ILE cc_start: 0.8494 (mt) cc_final: 0.8287 (mt) REVERT: E 41 ILE cc_start: 0.8599 (mt) cc_final: 0.8350 (tt) outliers start: 51 outliers final: 34 residues processed: 291 average time/residue: 0.2328 time to fit residues: 99.5525 Evaluate side-chains 272 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 306 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13612 Z= 0.282 Angle : 0.645 8.682 18454 Z= 0.337 Chirality : 0.043 0.200 2116 Planarity : 0.005 0.054 2306 Dihedral : 4.117 17.615 1852 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.12 % Allowed : 22.14 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1632 helix: 0.98 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.38 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.006 0.001 HIS C 306 PHE 0.023 0.002 PHE A 194 TYR 0.020 0.002 TYR B 188 ARG 0.005 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 243 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7474 (mm110) cc_final: 0.6810 (mm-40) REVERT: B 175 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6499 (t80) REVERT: B 418 ARG cc_start: 0.6481 (ptm-80) cc_final: 0.6071 (ttp80) REVERT: A 81 GLN cc_start: 0.6444 (mp10) cc_final: 0.5864 (mp10) REVERT: A 149 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.6161 (pm20) REVERT: A 170 ARG cc_start: 0.6329 (tpp-160) cc_final: 0.6006 (tpt170) REVERT: A 176 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 312 ILE cc_start: 0.8536 (mt) cc_final: 0.8328 (mt) REVERT: C 53 GLN cc_start: 0.7418 (mm110) cc_final: 0.6752 (mm-40) REVERT: C 175 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6501 (t80) REVERT: C 418 ARG cc_start: 0.6478 (ptm-80) cc_final: 0.6072 (ttp80) REVERT: D 81 GLN cc_start: 0.6467 (mp10) cc_final: 0.6004 (mp10) REVERT: D 149 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.6125 (pm20) REVERT: D 170 ARG cc_start: 0.6326 (tpp-160) cc_final: 0.6000 (tpt170) REVERT: D 176 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7599 (tm-30) outliers start: 59 outliers final: 46 residues processed: 287 average time/residue: 0.2351 time to fit residues: 98.9098 Evaluate side-chains 270 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 306 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 0.0070 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 0.0170 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN A 82 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS C 202 ASN D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13612 Z= 0.192 Angle : 0.613 8.927 18454 Z= 0.318 Chirality : 0.042 0.223 2116 Planarity : 0.004 0.052 2306 Dihedral : 3.953 16.676 1852 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.49 % Allowed : 22.84 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1632 helix: 1.11 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 172 HIS 0.003 0.001 HIS D 306 PHE 0.017 0.001 PHE B 343 TYR 0.016 0.001 TYR B 188 ARG 0.005 0.000 ARG D 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 251 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6749 (pp) REVERT: B 53 GLN cc_start: 0.7456 (mm110) cc_final: 0.6703 (mm-40) REVERT: B 97 ASN cc_start: 0.7791 (t0) cc_final: 0.7548 (t0) REVERT: B 175 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6516 (t80) REVERT: B 248 LEU cc_start: 0.7141 (tt) cc_final: 0.6909 (tp) REVERT: B 392 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8146 (mt) REVERT: B 418 ARG cc_start: 0.6425 (ptm-80) cc_final: 0.6045 (ttp80) REVERT: A 81 GLN cc_start: 0.6419 (mp10) cc_final: 0.5869 (mp10) REVERT: A 149 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.6035 (pm20) REVERT: A 170 ARG cc_start: 0.6371 (tpp-160) cc_final: 0.6038 (tpt170) REVERT: A 176 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7563 (tm-30) REVERT: J 41 ILE cc_start: 0.8574 (mt) cc_final: 0.8320 (tt) REVERT: C 51 ARG cc_start: 0.7622 (ppt170) cc_final: 0.7297 (ppt170) REVERT: C 53 GLN cc_start: 0.7436 (mm110) cc_final: 0.6769 (mm-40) REVERT: C 90 ASP cc_start: 0.7484 (m-30) cc_final: 0.7169 (m-30) REVERT: C 98 PHE cc_start: 0.8364 (t80) cc_final: 0.8069 (t80) REVERT: C 175 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6515 (t80) REVERT: C 248 LEU cc_start: 0.7049 (tt) cc_final: 0.6790 (tp) REVERT: C 392 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8296 (mt) REVERT: C 418 ARG cc_start: 0.6424 (ptm-80) cc_final: 0.6044 (ttp80) REVERT: D 81 GLN cc_start: 0.6450 (mp10) cc_final: 0.6008 (mp10) REVERT: D 149 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6035 (pm20) REVERT: D 170 ARG cc_start: 0.6372 (tpp-160) cc_final: 0.6039 (tpt170) REVERT: D 176 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7548 (tm-30) REVERT: E 41 ILE cc_start: 0.8582 (mt) cc_final: 0.8328 (tt) outliers start: 50 outliers final: 37 residues processed: 285 average time/residue: 0.2380 time to fit residues: 99.0221 Evaluate side-chains 271 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 306 HIS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13612 Z= 0.245 Angle : 0.636 8.982 18454 Z= 0.331 Chirality : 0.044 0.295 2116 Planarity : 0.005 0.053 2306 Dihedral : 4.008 16.484 1852 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.05 % Allowed : 23.32 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1632 helix: 1.10 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -2.27 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.004 0.001 HIS C 306 PHE 0.020 0.002 PHE A 194 TYR 0.018 0.001 TYR B 188 ARG 0.009 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 250 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6779 (pp) REVERT: B 53 GLN cc_start: 0.7432 (mm110) cc_final: 0.6723 (mm-40) REVERT: B 98 PHE cc_start: 0.8384 (t80) cc_final: 0.8139 (t80) REVERT: B 175 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6506 (t80) REVERT: B 248 LEU cc_start: 0.7160 (tt) cc_final: 0.6932 (tp) REVERT: B 392 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8251 (mt) REVERT: B 418 ARG cc_start: 0.6370 (ptm-80) cc_final: 0.5986 (ttp80) REVERT: A 81 GLN cc_start: 0.6260 (mp10) cc_final: 0.5677 (mp10) REVERT: A 110 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6946 (mm-30) REVERT: A 170 ARG cc_start: 0.6443 (tpp-160) cc_final: 0.6072 (tpt170) REVERT: A 176 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7530 (tm-30) REVERT: C 42 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6767 (pp) REVERT: C 51 ARG cc_start: 0.7632 (ppt170) cc_final: 0.7308 (ppt170) REVERT: C 53 GLN cc_start: 0.7442 (mm110) cc_final: 0.6700 (mm-40) REVERT: C 98 PHE cc_start: 0.8396 (t80) cc_final: 0.8084 (t80) REVERT: C 118 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7136 (tp30) REVERT: C 175 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6508 (t80) REVERT: C 248 LEU cc_start: 0.7155 (tt) cc_final: 0.6927 (tp) REVERT: C 418 ARG cc_start: 0.6366 (ptm-80) cc_final: 0.5989 (ttp80) REVERT: D 81 GLN cc_start: 0.6334 (mp10) cc_final: 0.5925 (mp10) REVERT: D 110 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6939 (mm-30) REVERT: D 170 ARG cc_start: 0.6444 (tpp-160) cc_final: 0.6071 (tpt170) REVERT: D 176 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7518 (tm-30) outliers start: 58 outliers final: 45 residues processed: 289 average time/residue: 0.2362 time to fit residues: 100.1876 Evaluate side-chains 286 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 0.0070 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS C 202 ASN D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13612 Z= 0.205 Angle : 0.626 10.166 18454 Z= 0.322 Chirality : 0.042 0.183 2116 Planarity : 0.005 0.055 2306 Dihedral : 3.956 15.884 1852 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.42 % Allowed : 24.02 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1632 helix: 1.22 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -2.27 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.004 0.001 HIS D 306 PHE 0.018 0.001 PHE D 194 TYR 0.017 0.001 TYR C 188 ARG 0.011 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 246 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7334 (mm110) cc_final: 0.6697 (mm-40) REVERT: B 90 ASP cc_start: 0.7483 (m-30) cc_final: 0.7088 (m-30) REVERT: B 97 ASN cc_start: 0.8045 (t0) cc_final: 0.7193 (t0) REVERT: B 98 PHE cc_start: 0.8302 (t80) cc_final: 0.7807 (t80) REVERT: B 118 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7119 (tp30) REVERT: B 175 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6554 (t80) REVERT: B 248 LEU cc_start: 0.7213 (tt) cc_final: 0.6923 (tp) REVERT: B 392 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 418 ARG cc_start: 0.6330 (ptm-80) cc_final: 0.5944 (ttp80) REVERT: B 421 LYS cc_start: 0.8319 (tmmt) cc_final: 0.8070 (ptmt) REVERT: A 81 GLN cc_start: 0.6302 (mp10) cc_final: 0.5751 (mp10) REVERT: A 110 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 170 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.6091 (tpt170) REVERT: A 176 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7509 (tm-30) REVERT: J 41 ILE cc_start: 0.8522 (mt) cc_final: 0.8249 (tt) REVERT: C 42 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6693 (pp) REVERT: C 51 ARG cc_start: 0.7682 (ppt170) cc_final: 0.7308 (ppt170) REVERT: C 53 GLN cc_start: 0.7417 (mm110) cc_final: 0.6669 (mm-40) REVERT: C 90 ASP cc_start: 0.7472 (m-30) cc_final: 0.7089 (m-30) REVERT: C 98 PHE cc_start: 0.8410 (t80) cc_final: 0.8101 (t80) REVERT: C 118 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7163 (tp30) REVERT: C 175 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6512 (t80) REVERT: C 248 LEU cc_start: 0.7154 (tt) cc_final: 0.6882 (tp) REVERT: C 418 ARG cc_start: 0.6331 (ptm-80) cc_final: 0.5971 (ttp80) REVERT: D 81 GLN cc_start: 0.6306 (mp10) cc_final: 0.5903 (mp10) REVERT: D 110 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6893 (mm-30) REVERT: D 170 ARG cc_start: 0.6465 (tpp-160) cc_final: 0.6091 (tpt170) REVERT: D 176 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 41 ILE cc_start: 0.8530 (mt) cc_final: 0.8258 (tt) outliers start: 49 outliers final: 41 residues processed: 280 average time/residue: 0.2430 time to fit residues: 98.5730 Evaluate side-chains 281 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13612 Z= 0.222 Angle : 0.639 9.069 18454 Z= 0.330 Chirality : 0.044 0.264 2116 Planarity : 0.005 0.052 2306 Dihedral : 3.982 16.664 1852 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.28 % Allowed : 23.81 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1632 helix: 1.26 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -2.22 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 172 HIS 0.004 0.001 HIS A 306 PHE 0.019 0.002 PHE A 121 TYR 0.018 0.001 TYR A 76 ARG 0.005 0.000 ARG C 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 243 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6756 (pp) REVERT: B 53 GLN cc_start: 0.7297 (mm110) cc_final: 0.6605 (mm-40) REVERT: B 98 PHE cc_start: 0.8365 (t80) cc_final: 0.8160 (t80) REVERT: B 118 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7131 (tp30) REVERT: B 175 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6574 (t80) REVERT: B 248 LEU cc_start: 0.7171 (tt) cc_final: 0.6946 (tp) REVERT: B 392 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (mt) REVERT: B 418 ARG cc_start: 0.6332 (ptm-80) cc_final: 0.5964 (ttp80) REVERT: A 81 GLN cc_start: 0.6330 (mp10) cc_final: 0.5778 (mp10) REVERT: A 110 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 170 ARG cc_start: 0.6495 (tpp-160) cc_final: 0.6136 (tpt170) REVERT: A 176 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 215 HIS cc_start: 0.1736 (p90) cc_final: 0.0576 (m90) REVERT: J 41 ILE cc_start: 0.8523 (mt) cc_final: 0.8257 (tt) REVERT: C 42 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6693 (pp) REVERT: C 51 ARG cc_start: 0.7682 (ppt170) cc_final: 0.7278 (ppt170) REVERT: C 53 GLN cc_start: 0.7345 (mm110) cc_final: 0.6600 (mm-40) REVERT: C 98 PHE cc_start: 0.8454 (t80) cc_final: 0.8163 (t80) REVERT: C 118 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7168 (tp30) REVERT: C 175 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6575 (t80) REVERT: C 248 LEU cc_start: 0.7292 (tt) cc_final: 0.7018 (tp) REVERT: C 418 ARG cc_start: 0.6336 (ptm-80) cc_final: 0.5969 (ttp80) REVERT: D 81 GLN cc_start: 0.6422 (mp10) cc_final: 0.5879 (mp10) REVERT: D 110 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6937 (mm-30) REVERT: D 170 ARG cc_start: 0.6492 (tpp-160) cc_final: 0.6134 (tpt170) REVERT: D 176 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7489 (tm-30) REVERT: D 215 HIS cc_start: 0.1761 (p90) cc_final: 0.0609 (m90) REVERT: D 312 ILE cc_start: 0.8536 (mt) cc_final: 0.8302 (mt) REVERT: E 41 ILE cc_start: 0.8529 (mt) cc_final: 0.8269 (tt) outliers start: 47 outliers final: 39 residues processed: 277 average time/residue: 0.2446 time to fit residues: 98.3653 Evaluate side-chains 279 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 111 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS D 82 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.147152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101533 restraints weight = 26728.577| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.73 r_work: 0.3180 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13612 Z= 0.188 Angle : 0.629 16.332 18454 Z= 0.320 Chirality : 0.042 0.182 2116 Planarity : 0.005 0.055 2306 Dihedral : 3.918 15.870 1852 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.07 % Allowed : 23.95 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1632 helix: 1.29 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -2.21 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.004 0.001 HIS A 306 PHE 0.022 0.001 PHE A 121 TYR 0.015 0.001 TYR B 188 ARG 0.004 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3132.01 seconds wall clock time: 57 minutes 40.40 seconds (3460.40 seconds total)