Starting phenix.real_space_refine on Thu Feb 15 05:19:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5j_23187/02_2024/7l5j_23187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5j_23187/02_2024/7l5j_23187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5j_23187/02_2024/7l5j_23187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5j_23187/02_2024/7l5j_23187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5j_23187/02_2024/7l5j_23187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l5j_23187/02_2024/7l5j_23187.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.083 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 44 5.16 5 C 7149 2.51 5 N 1873 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 142": "OD1" <-> "OD2" Residue "L ASP 169": "OD1" <-> "OD2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L ARG 187": "NH1" <-> "NH2" Residue "L TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 154": "OE1" <-> "OE2" Residue "X PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "X PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 142": "OD1" <-> "OD2" Residue "X ASP 169": "OD1" <-> "OD2" Residue "X GLU 186": "OE1" <-> "OE2" Residue "X ARG 187": "NH1" <-> "NH2" Residue "X TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 28": "OD1" <-> "OD2" Residue "Y TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11234 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2344 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 279} Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2338 Classifications: {'peptide': 304} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 278} Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1612 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "W" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1664 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Chain: "X" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1612 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "Y" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1664 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 204} Time building chain proxies: 6.29, per 1000 atoms: 0.56 Number of scatterers: 11234 At special positions: 0 Unit cell: (112.2, 121.55, 141.95, 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 44 16.00 O 2168 8.00 N 1873 7.00 C 7149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.04 Simple disulfide: pdb=" SG CYS W 146 " - pdb=" SG CYS W 201 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 87 " distance=2.04 Simple disulfide: pdb=" SG CYS X 133 " - pdb=" SG CYS X 193 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 146 " - pdb=" SG CYS Y 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 31 sheets defined 4.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.572A pdb=" N CYS A 240 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.770A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 removed outlier: 3.710A pdb=" N CYS B 240 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 removed outlier: 3.629A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.749A pdb=" N GLY L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 186 removed outlier: 4.211A pdb=" N TYR L 185 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 190 through 194 removed outlier: 3.668A pdb=" N TRP W 194 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 120 through 127 removed outlier: 3.749A pdb=" N GLY X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 181 through 186 removed outlier: 4.211A pdb=" N TYR X 185 " --> pdb=" O THR X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 194 removed outlier: 3.668A pdb=" N TRP Y 194 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 443 through 449 removed outlier: 3.835A pdb=" N ASP A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 447 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 431 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 433 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 507 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 289 through 293 removed outlier: 3.634A pdb=" N PHE A 289 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 291 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 293 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 339 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 475 removed outlier: 3.527A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 492 removed outlier: 4.329A pdb=" N TYR A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 448 through 449 removed outlier: 3.650A pdb=" N ARG B 433 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 507 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.792A pdb=" N VAL B 339 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 389 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 356 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 474 through 475 removed outlier: 3.756A pdb=" N SER B 519 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.668A pdb=" N THR L 5 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.704A pdb=" N GLU L 104 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.401A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 131 through 132 removed outlier: 4.193A pdb=" N VAL L 131 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 159 " --> pdb=" O THR L 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 143 through 146 Processing sheet with id=AB6, first strand: chain 'L' and resid 148 through 149 Processing sheet with id=AB7, first strand: chain 'W' and resid 3 through 5 Processing sheet with id=AB8, first strand: chain 'W' and resid 11 through 12 removed outlier: 3.543A pdb=" N VAL W 12 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET W 34 " --> pdb=" O GLN W 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP W 36 " --> pdb=" O ILE W 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 126 through 129 removed outlier: 4.028A pdb=" N LYS W 149 " --> pdb=" O SER W 126 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS W 149 " --> pdb=" O LEU W 183 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU W 183 " --> pdb=" O LYS W 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR W 182 " --> pdb=" O VAL W 175 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL W 175 " --> pdb=" O THR W 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 142 through 144 Processing sheet with id=AC2, first strand: chain 'W' and resid 157 through 160 Processing sheet with id=AC3, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.669A pdb=" N THR X 5 " --> pdb=" O SER X 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR X 70 " --> pdb=" O CYS X 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.705A pdb=" N GLU X 104 " --> pdb=" O MET X 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 52 through 53 removed outlier: 6.401A pdb=" N TRP X 34 " --> pdb=" O TRP X 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR X 84 " --> pdb=" O GLN X 37 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR X 96 " --> pdb=" O GLN X 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 131 through 132 removed outlier: 4.192A pdb=" N VAL X 131 " --> pdb=" O LEU X 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU X 159 " --> pdb=" O THR X 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 143 through 146 Processing sheet with id=AC8, first strand: chain 'X' and resid 148 through 149 Processing sheet with id=AC9, first strand: chain 'Y' and resid 3 through 5 Processing sheet with id=AD1, first strand: chain 'Y' and resid 11 through 12 removed outlier: 3.542A pdb=" N VAL Y 12 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET Y 34 " --> pdb=" O GLN Y 50 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 126 through 129 removed outlier: 4.029A pdb=" N LYS Y 149 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS Y 149 " --> pdb=" O LEU Y 183 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU Y 183 " --> pdb=" O LYS Y 149 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR Y 182 " --> pdb=" O VAL Y 175 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL Y 175 " --> pdb=" O THR Y 182 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 142 through 144 Processing sheet with id=AD4, first strand: chain 'Y' and resid 157 through 160 232 hydrogen bonds defined for protein. 576 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: 3.47 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3588 1.34 - 1.46: 2956 1.46 - 1.59: 4922 1.59 - 1.71: 0 1.71 - 1.84: 64 Bond restraints: 11530 Sorted by residual: bond pdb=" C ILE X 116 " pdb=" N PHE X 117 " ideal model delta sigma weight residual 1.332 1.355 -0.024 7.50e-03 1.78e+04 9.87e+00 bond pdb=" C ILE L 116 " pdb=" N PHE L 117 " ideal model delta sigma weight residual 1.332 1.355 -0.023 7.50e-03 1.78e+04 9.80e+00 bond pdb=" CB VAL A 271 " pdb=" CG1 VAL A 271 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 bond pdb=" CB GLU A 427 " pdb=" CG GLU A 427 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" CB GLN W 177 " pdb=" CG GLN W 177 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 11525 not shown) Histogram of bond angle deviations from ideal: 99.35 - 107.92: 709 107.92 - 116.49: 7413 116.49 - 125.07: 7379 125.07 - 133.64: 212 133.64 - 142.22: 31 Bond angle restraints: 15744 Sorted by residual: angle pdb=" C PHE A 423 " pdb=" N LEU A 424 " pdb=" CA LEU A 424 " ideal model delta sigma weight residual 120.69 142.22 -21.53 2.95e+00 1.15e-01 5.33e+01 angle pdb=" C GLN A 367 " pdb=" N ALA A 368 " pdb=" CA ALA A 368 " ideal model delta sigma weight residual 122.28 118.25 4.03 8.80e-01 1.29e+00 2.10e+01 angle pdb=" CA GLN X 155 " pdb=" CB GLN X 155 " pdb=" CG GLN X 155 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.01e+01 angle pdb=" CA GLN L 155 " pdb=" CB GLN L 155 " pdb=" CG GLN L 155 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA GLN Y 177 " pdb=" CB GLN Y 177 " pdb=" CG GLN Y 177 " ideal model delta sigma weight residual 114.10 122.54 -8.44 2.00e+00 2.50e-01 1.78e+01 ... (remaining 15739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6051 17.82 - 35.65: 534 35.65 - 53.47: 167 53.47 - 71.29: 85 71.29 - 89.12: 13 Dihedral angle restraints: 6850 sinusoidal: 2597 harmonic: 4253 Sorted by residual: dihedral pdb=" CA TYR W 104 " pdb=" C TYR W 104 " pdb=" N ALA W 105 " pdb=" CA ALA W 105 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR Y 104 " pdb=" C TYR Y 104 " pdb=" N ALA Y 105 " pdb=" CA ALA Y 105 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLY A 302 " pdb=" C GLY A 302 " pdb=" N GLU A 303 " pdb=" CA GLU A 303 " ideal model delta harmonic sigma weight residual 180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 6847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1106 0.038 - 0.077: 470 0.077 - 0.115: 157 0.115 - 0.153: 35 0.153 - 0.192: 3 Chirality restraints: 1771 Sorted by residual: chirality pdb=" CA ARG W 134 " pdb=" N ARG W 134 " pdb=" C ARG W 134 " pdb=" CB ARG W 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA ARG Y 134 " pdb=" N ARG Y 134 " pdb=" C ARG Y 134 " pdb=" CB ARG Y 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ASN A 364 " pdb=" N ASN A 364 " pdb=" C ASN A 364 " pdb=" CB ASN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 1768 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE X 149 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ILE X 149 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE X 149 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP X 150 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 149 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C ILE L 149 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE L 149 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP L 150 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 496 " 0.023 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR B 496 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 496 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 496 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 496 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 496 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 496 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 496 " 0.004 2.00e-02 2.50e+03 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 417 2.66 - 3.22: 10811 3.22 - 3.78: 15754 3.78 - 4.34: 21103 4.34 - 4.90: 35604 Nonbonded interactions: 83689 Sorted by model distance: nonbonded pdb=" O PHE X 138 " pdb=" OG1 THR X 171 " model vdw 2.099 2.440 nonbonded pdb=" O PHE L 138 " pdb=" OG1 THR L 171 " model vdw 2.100 2.440 nonbonded pdb=" OG SER W 208 " pdb=" OG1 THR W 210 " model vdw 2.122 2.440 nonbonded pdb=" OG SER Y 208 " pdb=" OG1 THR Y 210 " model vdw 2.123 2.440 nonbonded pdb=" O GLN L 123 " pdb=" OG SER L 126 " model vdw 2.145 2.440 ... (remaining 83684 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 228 through 531) selection = chain 'B' } ncs_group { reference = chain 'L' selection = chain 'X' } ncs_group { reference = chain 'W' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 4.260 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.330 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.008 0.063 11530 Z= 0.505 Angle : 0.881 21.527 15744 Z= 0.467 Chirality : 0.047 0.192 1771 Planarity : 0.005 0.046 2019 Dihedral : 17.033 89.118 4104 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.40 % Favored : 83.53 % Rotamer: Outliers : 8.54 % Allowed : 8.30 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -5.48 (0.18), residues: 1457 helix: -3.12 (0.61), residues: 34 sheet: -3.14 (0.20), residues: 510 loop : -4.20 (0.16), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 460 HIS 0.003 0.001 HIS B 270 PHE 0.012 0.002 PHE W 172 TYR 0.029 0.002 TYR B 496 ARG 0.008 0.001 ARG Y 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 273 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.6290 (tpt) cc_final: 0.6004 (tpt) REVERT: A 385 ASP cc_start: 0.7987 (t0) cc_final: 0.7710 (t0) REVERT: A 516 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 521 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7595 (m) REVERT: B 345 LYS cc_start: 0.8207 (ptmm) cc_final: 0.7708 (pttp) REVERT: B 366 ASP cc_start: 0.5737 (m-30) cc_final: 0.5377 (t0) REVERT: B 476 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7065 (ttm-80) REVERT: L 11 MET cc_start: 0.6431 (ppp) cc_final: 0.6177 (ppp) REVERT: L 26 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7189 (m) REVERT: L 146 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.5950 (tttt) REVERT: L 159 LEU cc_start: 0.6532 (tt) cc_final: 0.6148 (tt) REVERT: W 6 GLU cc_start: 0.7425 (mp0) cc_final: 0.7219 (mt-10) REVERT: W 89 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7760 (tm-30) REVERT: W 90 ASP cc_start: 0.7478 (m-30) cc_final: 0.6987 (m-30) REVERT: W 93 LEU cc_start: 0.7669 (mm) cc_final: 0.7398 (mt) REVERT: W 103 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7584 (p90) REVERT: W 142 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6889 (m) REVERT: X 11 MET cc_start: 0.6616 (ppp) cc_final: 0.6007 (ppp) REVERT: X 31 TYR cc_start: 0.8007 (m-80) cc_final: 0.7772 (m-80) REVERT: X 121 SER cc_start: 0.5655 (OUTLIER) cc_final: 0.5353 (m) REVERT: X 178 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5987 (tt) REVERT: X 179 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.5680 (p) REVERT: Y 121 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7366 (ttmt) REVERT: Y 142 VAL cc_start: 0.4919 (OUTLIER) cc_final: 0.4446 (m) REVERT: Y 160 TRP cc_start: 0.8027 (m100) cc_final: 0.7088 (m100) REVERT: Y 177 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5461 (pt0) REVERT: Y 184 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7193 (t) outliers start: 105 outliers final: 23 residues processed: 361 average time/residue: 0.2426 time to fit residues: 121.9785 Evaluate side-chains 199 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 88 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 141 MET Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 162 SER Chi-restraints excluded: chain W residue 182 THR Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 208 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 121 SER Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 179 THR Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 121 LYS Chi-restraints excluded: chain Y residue 142 VAL Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 184 SER Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 210 THR Chi-restraints excluded: chain Y residue 214 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 526 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN L 188 HIS ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 82 GLN W 161 ASN ** X 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 136 ASN X 188 HIS Y 39 GLN Y 111 GLN ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11530 Z= 0.259 Angle : 0.696 9.391 15744 Z= 0.355 Chirality : 0.046 0.272 1771 Planarity : 0.005 0.039 2019 Dihedral : 8.156 89.666 1650 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 4.39 % Allowed : 17.33 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.18 (0.20), residues: 1457 helix: -1.01 (0.86), residues: 36 sheet: -2.51 (0.21), residues: 517 loop : -3.15 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 460 HIS 0.003 0.001 HIS L 188 PHE 0.020 0.002 PHE A 509 TYR 0.016 0.002 TYR Y 94 ARG 0.004 0.001 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 229 MET cc_start: 0.6411 (tpt) cc_final: 0.6207 (tpt) REVERT: A 296 GLU cc_start: 0.6774 (pm20) cc_final: 0.6569 (pm20) REVERT: A 356 GLU cc_start: 0.6741 (tt0) cc_final: 0.6538 (tt0) REVERT: A 385 ASP cc_start: 0.7967 (t0) cc_final: 0.7714 (t0) REVERT: A 402 GLN cc_start: 0.8108 (tt0) cc_final: 0.7788 (pt0) REVERT: B 238 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7207 (ttm110) REVERT: B 345 LYS cc_start: 0.8300 (ptmm) cc_final: 0.7943 (tmtt) REVERT: B 366 ASP cc_start: 0.6008 (m-30) cc_final: 0.5504 (t70) REVERT: B 476 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7262 (ttm110) REVERT: W 89 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7683 (tm-30) REVERT: W 93 LEU cc_start: 0.7681 (mm) cc_final: 0.7475 (mt) REVERT: W 103 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7617 (p90) REVERT: W 142 VAL cc_start: 0.7030 (OUTLIER) cc_final: 0.6798 (m) REVERT: W 201 CYS cc_start: 0.7483 (OUTLIER) cc_final: 0.5878 (m) REVERT: X 11 MET cc_start: 0.7356 (ppp) cc_final: 0.7018 (tmm) REVERT: X 32 MET cc_start: 0.7390 (mtt) cc_final: 0.6821 (mtt) REVERT: X 104 GLU cc_start: 0.7315 (pm20) cc_final: 0.7091 (pm20) REVERT: X 138 PHE cc_start: 0.8007 (p90) cc_final: 0.7476 (p90) REVERT: X 146 LYS cc_start: 0.7151 (ptpp) cc_final: 0.6893 (ptmt) REVERT: X 159 LEU cc_start: 0.7496 (pp) cc_final: 0.7225 (pt) REVERT: Y 22 CYS cc_start: 0.5951 (t) cc_final: 0.5154 (t) REVERT: Y 82 GLN cc_start: 0.7334 (tp40) cc_final: 0.7029 (tp-100) REVERT: Y 177 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.5825 (pt0) outliers start: 54 outliers final: 26 residues processed: 221 average time/residue: 0.2170 time to fit residues: 70.8044 Evaluate side-chains 190 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 162 SER Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 0.0070 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 484 GLN B 261 ASN B 265 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN X 37 GLN X 137 ASN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11530 Z= 0.296 Angle : 0.670 9.520 15744 Z= 0.339 Chirality : 0.045 0.228 1771 Planarity : 0.005 0.037 2019 Dihedral : 6.499 85.970 1608 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 5.78 % Allowed : 19.61 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -3.64 (0.20), residues: 1457 helix: -1.04 (0.87), residues: 37 sheet: -2.16 (0.22), residues: 506 loop : -2.74 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 460 HIS 0.003 0.001 HIS X 33 PHE 0.013 0.002 PHE W 152 TYR 0.015 0.001 TYR Y 94 ARG 0.004 0.000 ARG W 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 159 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 385 ASP cc_start: 0.7984 (t0) cc_final: 0.7754 (t0) REVERT: A 486 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6586 (mp) REVERT: B 345 LYS cc_start: 0.8212 (ptmm) cc_final: 0.7902 (tmtt) REVERT: B 366 ASP cc_start: 0.6101 (m-30) cc_final: 0.5534 (t70) REVERT: B 476 ARG cc_start: 0.7530 (mtm110) cc_final: 0.7153 (ttm110) REVERT: W 89 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7621 (tm-30) REVERT: W 93 LEU cc_start: 0.7739 (mm) cc_final: 0.7479 (mt) REVERT: W 103 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7519 (p90) REVERT: W 142 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6567 (p) REVERT: W 201 CYS cc_start: 0.7391 (OUTLIER) cc_final: 0.5824 (m) REVERT: X 11 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7106 (ppp) REVERT: X 32 MET cc_start: 0.7742 (mtt) cc_final: 0.7011 (mtt) REVERT: X 104 GLU cc_start: 0.7500 (pm20) cc_final: 0.7261 (pm20) REVERT: X 188 HIS cc_start: 0.2171 (OUTLIER) cc_final: 0.1768 (t70) REVERT: X 209 ASN cc_start: 0.5685 (OUTLIER) cc_final: 0.4688 (t0) REVERT: Y 6 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7310 (mm-30) REVERT: Y 160 TRP cc_start: 0.8270 (m100) cc_final: 0.7647 (m100) REVERT: Y 177 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5567 (pt0) outliers start: 71 outliers final: 43 residues processed: 220 average time/residue: 0.1968 time to fit residues: 65.1299 Evaluate side-chains 194 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 18 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 162 SER Chi-restraints excluded: chain W residue 193 SER Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 188 HIS Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 14 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11530 Z= 0.195 Angle : 0.610 10.473 15744 Z= 0.304 Chirality : 0.043 0.161 1771 Planarity : 0.004 0.063 2019 Dihedral : 5.816 88.036 1606 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.39 % Allowed : 21.81 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -3.25 (0.21), residues: 1457 helix: -0.76 (0.87), residues: 37 sheet: -1.97 (0.22), residues: 523 loop : -2.41 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 460 HIS 0.002 0.000 HIS Y 170 PHE 0.011 0.001 PHE W 152 TYR 0.009 0.001 TYR Y 108 ARG 0.006 0.000 ARG Y 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 156 time to evaluate : 1.425 Fit side-chains REVERT: A 490 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7521 (mtmm) REVERT: B 345 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7693 (pttp) REVERT: B 366 ASP cc_start: 0.5974 (m-30) cc_final: 0.5388 (t70) REVERT: B 436 MET cc_start: 0.8136 (mtp) cc_final: 0.7917 (mtt) REVERT: B 476 ARG cc_start: 0.7390 (mtm110) cc_final: 0.7025 (ttm110) REVERT: L 166 ASP cc_start: 0.8182 (m-30) cc_final: 0.7604 (t0) REVERT: W 89 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7679 (tm-30) REVERT: W 93 LEU cc_start: 0.7717 (mm) cc_final: 0.7467 (mt) REVERT: W 103 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7410 (p90) REVERT: W 142 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6720 (p) REVERT: W 201 CYS cc_start: 0.7360 (OUTLIER) cc_final: 0.5748 (m) REVERT: X 32 MET cc_start: 0.7792 (mtt) cc_final: 0.7018 (mtt) REVERT: X 104 GLU cc_start: 0.7504 (pm20) cc_final: 0.7177 (pm20) REVERT: X 138 PHE cc_start: 0.8169 (p90) cc_final: 0.7630 (p90) REVERT: X 209 ASN cc_start: 0.5506 (OUTLIER) cc_final: 0.4642 (t0) REVERT: Y 82 GLN cc_start: 0.7551 (tp40) cc_final: 0.7205 (tp-100) REVERT: Y 91 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7852 (t) REVERT: Y 160 TRP cc_start: 0.8212 (m100) cc_final: 0.7623 (m100) REVERT: Y 177 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.5480 (pt0) outliers start: 54 outliers final: 39 residues processed: 199 average time/residue: 0.1974 time to fit residues: 58.7751 Evaluate side-chains 192 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain W residue 18 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain X residue 209 ASN Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 91 THR Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 177 GLN Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.0670 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN W 82 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11530 Z= 0.238 Angle : 0.619 9.572 15744 Z= 0.309 Chirality : 0.044 0.150 1771 Planarity : 0.004 0.048 2019 Dihedral : 5.612 85.322 1604 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 5.70 % Allowed : 20.99 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.99 (0.21), residues: 1457 helix: -0.61 (0.89), residues: 37 sheet: -1.68 (0.22), residues: 515 loop : -2.31 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 460 HIS 0.009 0.001 HIS X 188 PHE 0.018 0.001 PHE A 401 TYR 0.010 0.001 TYR Y 94 ARG 0.004 0.000 ARG Y 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 158 time to evaluate : 1.327 Fit side-chains REVERT: B 238 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7667 (ttm110) REVERT: B 345 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7694 (pttp) REVERT: B 366 ASP cc_start: 0.6077 (m-30) cc_final: 0.5474 (t70) REVERT: B 473 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.5880 (tt) REVERT: B 476 ARG cc_start: 0.7350 (mtm110) cc_final: 0.6964 (ttm110) REVERT: L 166 ASP cc_start: 0.8170 (m-30) cc_final: 0.7522 (t0) REVERT: W 57 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8203 (p) REVERT: W 76 LYS cc_start: 0.5928 (mttp) cc_final: 0.5663 (mttp) REVERT: W 89 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7687 (tm-30) REVERT: W 93 LEU cc_start: 0.7724 (mm) cc_final: 0.7464 (mt) REVERT: W 103 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7393 (p90) REVERT: W 142 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.6863 (p) REVERT: W 201 CYS cc_start: 0.7252 (OUTLIER) cc_final: 0.5541 (m) REVERT: X 138 PHE cc_start: 0.8286 (p90) cc_final: 0.7726 (p90) REVERT: Y 82 GLN cc_start: 0.7572 (tp40) cc_final: 0.7218 (tp-100) REVERT: Y 160 TRP cc_start: 0.8153 (m100) cc_final: 0.7568 (m100) outliers start: 70 outliers final: 47 residues processed: 208 average time/residue: 0.2071 time to fit residues: 64.5511 Evaluate side-chains 202 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 18 LEU Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 0.0010 chunk 141 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 50 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 209 ASN ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11530 Z= 0.149 Angle : 0.572 9.978 15744 Z= 0.283 Chirality : 0.043 0.143 1771 Planarity : 0.004 0.040 2019 Dihedral : 4.674 42.443 1598 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.07 % Allowed : 23.27 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.61 (0.21), residues: 1457 helix: -0.44 (0.90), residues: 37 sheet: -1.39 (0.23), residues: 521 loop : -2.06 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 47 HIS 0.005 0.001 HIS X 188 PHE 0.010 0.001 PHE L 134 TYR 0.008 0.001 TYR Y 151 ARG 0.004 0.000 ARG Y 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 169 time to evaluate : 1.389 Fit side-chains REVERT: B 238 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7612 (ttm110) REVERT: B 345 LYS cc_start: 0.8086 (ptmm) cc_final: 0.7651 (pttp) REVERT: B 366 ASP cc_start: 0.6225 (m-30) cc_final: 0.5592 (t70) REVERT: B 473 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.5775 (tt) REVERT: B 476 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7051 (ttm110) REVERT: L 52 ASN cc_start: 0.6446 (m-40) cc_final: 0.6215 (m110) REVERT: L 166 ASP cc_start: 0.8158 (m-30) cc_final: 0.7656 (m-30) REVERT: W 57 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8200 (p) REVERT: W 76 LYS cc_start: 0.6028 (mttp) cc_final: 0.5769 (mttp) REVERT: W 89 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7679 (tm-30) REVERT: W 93 LEU cc_start: 0.7741 (mm) cc_final: 0.7513 (mt) REVERT: W 103 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7436 (p90) REVERT: W 141 MET cc_start: 0.5743 (tpp) cc_final: 0.5489 (tpp) REVERT: W 142 VAL cc_start: 0.7270 (OUTLIER) cc_final: 0.6881 (p) REVERT: W 201 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.5517 (m) REVERT: X 32 MET cc_start: 0.7783 (mtt) cc_final: 0.7048 (mtt) REVERT: X 78 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7306 (mt-10) REVERT: X 104 GLU cc_start: 0.7975 (pm20) cc_final: 0.7689 (pm20) REVERT: X 138 PHE cc_start: 0.8208 (p90) cc_final: 0.7687 (p90) REVERT: X 160 ASN cc_start: 0.6810 (p0) cc_final: 0.5511 (m-40) REVERT: Y 160 TRP cc_start: 0.8130 (m100) cc_final: 0.7561 (m100) outliers start: 50 outliers final: 34 residues processed: 206 average time/residue: 0.2062 time to fit residues: 62.6143 Evaluate side-chains 191 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 116 ILE Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 GLN X 155 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 11530 Z= 0.502 Angle : 0.761 9.749 15744 Z= 0.389 Chirality : 0.047 0.167 1771 Planarity : 0.005 0.044 2019 Dihedral : 5.719 35.795 1598 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 5.86 % Allowed : 22.78 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.91 (0.21), residues: 1457 helix: -0.83 (0.84), residues: 37 sheet: -1.49 (0.23), residues: 526 loop : -2.35 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 285 HIS 0.005 0.002 HIS A 242 PHE 0.015 0.002 PHE X 95 TYR 0.022 0.002 TYR X 85 ARG 0.004 0.001 ARG L 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 149 time to evaluate : 1.196 Fit side-chains REVERT: B 345 LYS cc_start: 0.8202 (ptmm) cc_final: 0.7973 (tmtt) REVERT: B 476 ARG cc_start: 0.7374 (mtm110) cc_final: 0.6934 (ttm110) REVERT: L 76 ARG cc_start: 0.6330 (mmt180) cc_final: 0.5916 (mmp80) REVERT: L 166 ASP cc_start: 0.8406 (m-30) cc_final: 0.7709 (t70) REVERT: W 76 LYS cc_start: 0.6240 (mttp) cc_final: 0.5938 (mttp) REVERT: W 89 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7668 (tm-30) REVERT: W 93 LEU cc_start: 0.7778 (mm) cc_final: 0.7444 (mt) REVERT: W 103 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7327 (p90) REVERT: W 201 CYS cc_start: 0.7301 (OUTLIER) cc_final: 0.5575 (m) REVERT: X 78 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7472 (mt-10) REVERT: X 89 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8262 (pp30) REVERT: X 104 GLU cc_start: 0.8039 (pm20) cc_final: 0.7765 (pm20) REVERT: X 138 PHE cc_start: 0.8422 (p90) cc_final: 0.7694 (p90) REVERT: X 160 ASN cc_start: 0.6995 (p0) cc_final: 0.5819 (m-40) REVERT: X 167 SER cc_start: 0.4622 (OUTLIER) cc_final: 0.4167 (p) REVERT: Y 122 THR cc_start: 0.8160 (p) cc_final: 0.7931 (m) REVERT: Y 160 TRP cc_start: 0.8121 (m100) cc_final: 0.7702 (m100) outliers start: 72 outliers final: 54 residues processed: 204 average time/residue: 0.1974 time to fit residues: 59.7922 Evaluate side-chains 202 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 144 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 167 SER Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 209 ASN ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11530 Z= 0.194 Angle : 0.616 10.349 15744 Z= 0.310 Chirality : 0.044 0.358 1771 Planarity : 0.004 0.043 2019 Dihedral : 4.986 41.595 1597 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.39 % Allowed : 24.57 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.61 (0.21), residues: 1457 helix: -0.53 (0.87), residues: 37 sheet: -1.33 (0.23), residues: 497 loop : -2.10 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.004 0.001 HIS X 33 PHE 0.010 0.001 PHE W 152 TYR 0.011 0.001 TYR L 93 ARG 0.004 0.000 ARG X 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 155 time to evaluate : 1.305 Fit side-chains REVERT: B 238 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7244 (ttm110) REVERT: B 345 LYS cc_start: 0.8135 (ptmm) cc_final: 0.7688 (pttp) REVERT: B 473 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.5948 (tt) REVERT: B 476 ARG cc_start: 0.7358 (mtm110) cc_final: 0.7042 (ttm110) REVERT: L 76 ARG cc_start: 0.6204 (mmt180) cc_final: 0.5424 (mmp80) REVERT: L 166 ASP cc_start: 0.8245 (m-30) cc_final: 0.7573 (t70) REVERT: W 18 LEU cc_start: 0.8073 (mt) cc_final: 0.7599 (mp) REVERT: W 76 LYS cc_start: 0.6225 (mttp) cc_final: 0.5929 (mttp) REVERT: W 89 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7701 (tm-30) REVERT: W 93 LEU cc_start: 0.7589 (mm) cc_final: 0.7321 (mt) REVERT: W 103 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7408 (p90) REVERT: X 78 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7347 (mt-10) REVERT: X 138 PHE cc_start: 0.8263 (p90) cc_final: 0.7562 (p90) REVERT: X 160 ASN cc_start: 0.7025 (p0) cc_final: 0.5823 (m-40) REVERT: Y 160 TRP cc_start: 0.8054 (m100) cc_final: 0.7623 (m100) REVERT: Y 200 THR cc_start: 0.6497 (p) cc_final: 0.6249 (t) outliers start: 54 outliers final: 47 residues processed: 195 average time/residue: 0.2039 time to fit residues: 59.4250 Evaluate side-chains 198 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 149 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 201 CYS Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.2980 chunk 122 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 GLN ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11530 Z= 0.174 Angle : 0.594 10.346 15744 Z= 0.297 Chirality : 0.044 0.340 1771 Planarity : 0.004 0.041 2019 Dihedral : 4.724 40.122 1597 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.91 % Allowed : 25.06 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.40 (0.22), residues: 1457 helix: -0.39 (0.87), residues: 37 sheet: -1.20 (0.24), residues: 489 loop : -1.94 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 46 HIS 0.003 0.001 HIS B 242 PHE 0.014 0.001 PHE A 401 TYR 0.025 0.001 TYR L 48 ARG 0.003 0.000 ARG W 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 148 time to evaluate : 1.389 Fit side-chains REVERT: B 345 LYS cc_start: 0.8118 (ptmm) cc_final: 0.7676 (pttp) REVERT: B 473 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.5929 (tt) REVERT: B 476 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7133 (ttm110) REVERT: L 166 ASP cc_start: 0.8257 (m-30) cc_final: 0.7589 (t70) REVERT: W 18 LEU cc_start: 0.8076 (mt) cc_final: 0.7546 (mp) REVERT: W 76 LYS cc_start: 0.6323 (mttp) cc_final: 0.6041 (mttp) REVERT: W 89 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7679 (tm-30) REVERT: W 93 LEU cc_start: 0.7592 (mm) cc_final: 0.7353 (mt) REVERT: W 103 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7262 (p90) REVERT: X 78 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7331 (mt-10) REVERT: X 89 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: X 138 PHE cc_start: 0.8200 (p90) cc_final: 0.7694 (p90) REVERT: X 160 ASN cc_start: 0.6966 (p0) cc_final: 0.5647 (m-40) REVERT: Y 160 TRP cc_start: 0.8008 (m100) cc_final: 0.7563 (m100) REVERT: Y 200 THR cc_start: 0.6521 (p) cc_final: 0.6292 (t) outliers start: 48 outliers final: 40 residues processed: 180 average time/residue: 0.1991 time to fit residues: 53.7371 Evaluate side-chains 189 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 111 GLN ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11530 Z= 0.237 Angle : 0.620 10.451 15744 Z= 0.310 Chirality : 0.044 0.328 1771 Planarity : 0.004 0.044 2019 Dihedral : 4.821 39.118 1597 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 4.23 % Allowed : 25.22 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.37 (0.22), residues: 1457 helix: -0.23 (0.87), residues: 37 sheet: -1.17 (0.24), residues: 493 loop : -1.93 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 46 HIS 0.002 0.001 HIS X 188 PHE 0.009 0.001 PHE B 289 TYR 0.022 0.001 TYR L 48 ARG 0.003 0.000 ARG X 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 1.267 Fit side-chains REVERT: A 238 ARG cc_start: 0.7833 (ptm160) cc_final: 0.7378 (ttp-110) REVERT: A 402 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: B 345 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7694 (pttp) REVERT: B 473 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6001 (tt) REVERT: B 476 ARG cc_start: 0.7398 (mtm110) cc_final: 0.7088 (ttm110) REVERT: L 76 ARG cc_start: 0.6217 (mmt180) cc_final: 0.5429 (mmp80) REVERT: L 166 ASP cc_start: 0.8233 (m-30) cc_final: 0.7563 (t70) REVERT: W 18 LEU cc_start: 0.8067 (mt) cc_final: 0.7784 (mt) REVERT: W 76 LYS cc_start: 0.6390 (mttp) cc_final: 0.6084 (mttp) REVERT: W 89 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7685 (tm-30) REVERT: W 93 LEU cc_start: 0.7640 (mm) cc_final: 0.7373 (mt) REVERT: W 103 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7338 (p90) REVERT: X 78 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7382 (mt-10) REVERT: X 138 PHE cc_start: 0.8239 (p90) cc_final: 0.7703 (p90) REVERT: X 160 ASN cc_start: 0.7057 (p0) cc_final: 0.5819 (m-40) REVERT: Y 134 ARG cc_start: 0.2353 (OUTLIER) cc_final: 0.1830 (ttm110) REVERT: Y 160 TRP cc_start: 0.8050 (m100) cc_final: 0.7633 (m100) REVERT: Y 200 THR cc_start: 0.6439 (p) cc_final: 0.6172 (t) outliers start: 52 outliers final: 43 residues processed: 183 average time/residue: 0.2129 time to fit residues: 57.4141 Evaluate side-chains 194 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 55 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 71 SER Chi-restraints excluded: chain W residue 103 PHE Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 202 ASN Chi-restraints excluded: chain W residue 203 VAL Chi-restraints excluded: chain W residue 210 THR Chi-restraints excluded: chain X residue 10 ILE Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 75 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 196 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 103 PHE Chi-restraints excluded: chain Y residue 134 ARG Chi-restraints excluded: chain Y residue 146 CYS Chi-restraints excluded: chain Y residue 182 THR Chi-restraints excluded: chain Y residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 17 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 48 optimal weight: 0.0270 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 402 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.184443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.127649 restraints weight = 15652.687| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.63 r_work: 0.3562 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11530 Z= 0.151 Angle : 0.579 10.611 15744 Z= 0.287 Chirality : 0.043 0.325 1771 Planarity : 0.004 0.042 2019 Dihedral : 4.511 41.160 1597 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.74 % Allowed : 25.71 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.15 % 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: -2.14 (0.22), residues: 1457 helix: -0.04 (0.89), residues: 37 sheet: -0.98 (0.24), residues: 503 loop : -1.80 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 46 HIS 0.003 0.001 HIS B 242 PHE 0.009 0.001 PHE B 466 TYR 0.025 0.001 TYR L 48 ARG 0.002 0.000 ARG W 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.35 seconds wall clock time: 51 minutes 20.32 seconds (3080.32 seconds total)