Starting phenix.real_space_refine on Sun Mar 10 22:52:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wus_32840/03_2024/7wus_32840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wus_32840/03_2024/7wus_32840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wus_32840/03_2024/7wus_32840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wus_32840/03_2024/7wus_32840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wus_32840/03_2024/7wus_32840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wus_32840/03_2024/7wus_32840.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 336 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3446 2.51 5 N 946 2.21 5 O 1016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5450 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 319} Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 319} Time building chain proxies: 3.27, per 1000 atoms: 0.60 Number of scatterers: 5450 At special positions: 0 Unit cell: (105.6, 101.64, 67.32, 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 42 16.00 O 1016 8.00 N 946 7.00 C 3446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " 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: 1.84 Conformation dependent library (CDL) restraints added in 935.3 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 16.1% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 38 through 50 removed outlier: 4.242A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.653A pdb=" N LYS A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.574A pdb=" N ASN A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 removed outlier: 4.242A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.652A pdb=" N LYS B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.575A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.561A pdb=" N GLU A 12 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS A 4 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS B 4 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 12 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 removed outlier: 7.483A pdb=" N GLN A 35 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.267A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 removed outlier: 5.213A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 216 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 186 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 186 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 216 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36 removed outlier: 7.484A pdb=" N GLN B 35 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.267A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N MET B 89 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 324 118 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1762 1.34 - 1.46: 1309 1.46 - 1.58: 2463 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 5594 Sorted by residual: bond pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" C PRO A 106 " pdb=" N GLN A 107 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.40e-02 5.10e+03 1.95e+00 bond pdb=" C PRO B 106 " pdb=" N GLN B 107 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.64e+00 bond pdb=" CA TYR B 32 " pdb=" C TYR B 32 " ideal model delta sigma weight residual 1.523 1.538 -0.014 1.30e-02 5.92e+03 1.22e+00 ... (remaining 5589 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 192 106.72 - 113.55: 3050 113.55 - 120.38: 1898 120.38 - 127.20: 2330 127.20 - 134.03: 110 Bond angle restraints: 7580 Sorted by residual: angle pdb=" C PRO B 106 " pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 121.70 133.34 -11.64 1.80e+00 3.09e-01 4.18e+01 angle pdb=" C PRO A 106 " pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C TYR B 32 " pdb=" N LYS B 33 " pdb=" CA LYS B 33 " ideal model delta sigma weight residual 121.70 131.65 -9.95 1.80e+00 3.09e-01 3.06e+01 angle pdb=" C TYR A 32 " pdb=" N LYS A 33 " pdb=" CA LYS A 33 " ideal model delta sigma weight residual 121.70 131.63 -9.93 1.80e+00 3.09e-01 3.04e+01 angle pdb=" C LYS B 189 " pdb=" N ASP B 190 " pdb=" CA ASP B 190 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 ... (remaining 7575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 2734 16.00 - 32.00: 466 32.00 - 48.00: 124 48.00 - 64.00: 22 64.00 - 80.00: 10 Dihedral angle restraints: 3356 sinusoidal: 1396 harmonic: 1960 Sorted by residual: dihedral pdb=" CA GLN B 31 " pdb=" C GLN B 31 " pdb=" N TYR B 32 " pdb=" CA TYR B 32 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLN A 31 " pdb=" C GLN A 31 " pdb=" N TYR A 32 " pdb=" CA TYR A 32 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 312 " pdb=" CB CYS B 312 " ideal model delta sinusoidal sigma weight residual 93.00 54.60 38.40 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 3353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 628 0.047 - 0.093: 129 0.093 - 0.140: 41 0.140 - 0.186: 6 0.186 - 0.233: 4 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA GLN A 107 " pdb=" N GLN A 107 " pdb=" C GLN A 107 " pdb=" CB GLN A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLN B 107 " pdb=" N GLN B 107 " pdb=" C GLN B 107 " pdb=" CB GLN B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 167 " pdb=" CA ILE A 167 " pdb=" CG1 ILE A 167 " pdb=" CG2 ILE A 167 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 805 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 189 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C LYS A 189 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS A 189 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 190 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 189 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LYS B 189 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS B 189 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP B 190 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 277 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 pdb=" C PHE A 277 " -0.019 2.00e-02 2.50e+03 pdb=" O PHE A 277 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP A 278 " 0.006 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1513 2.80 - 3.33: 4826 3.33 - 3.85: 8758 3.85 - 4.38: 9812 4.38 - 4.90: 16744 Nonbonded interactions: 41653 Sorted by model distance: nonbonded pdb=" O THR B 164 " pdb=" OG1 THR B 165 " model vdw 2.275 2.440 nonbonded pdb=" O THR A 164 " pdb=" OG1 THR A 165 " model vdw 2.276 2.440 nonbonded pdb=" O ARG A 105 " pdb=" NE2 GLN A 107 " model vdw 2.287 2.520 nonbonded pdb=" O ARG B 105 " pdb=" NE2 GLN B 107 " model vdw 2.288 2.520 nonbonded pdb=" OD1 ASP A 176 " pdb=" N PHE A 178 " model vdw 2.295 2.520 ... (remaining 41648 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' selection = chain 'B' } 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 1.180 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5594 Z= 0.170 Angle : 0.748 11.636 7580 Z= 0.404 Chirality : 0.046 0.233 808 Planarity : 0.004 0.038 962 Dihedral : 17.105 79.998 2056 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.00 % Allowed : 24.08 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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 (0.32), residues: 678 helix: -0.05 (0.70), residues: 64 sheet: -1.82 (0.40), residues: 156 loop : -1.82 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 225 HIS 0.002 0.000 HIS A 195 PHE 0.009 0.001 PHE B 217 TYR 0.012 0.001 TYR B 32 ARG 0.009 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 PHE cc_start: 0.7575 (m-80) cc_final: 0.7175 (m-80) REVERT: B 35 GLN cc_start: 0.7206 (pt0) cc_final: 0.6988 (pt0) REVERT: B 62 ARG cc_start: 0.7403 (ptp-110) cc_final: 0.7115 (ttt-90) REVERT: B 232 TRP cc_start: 0.8435 (t60) cc_final: 0.8181 (t60) outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.2249 time to fit residues: 35.7729 Evaluate side-chains 88 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 31 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 70 GLN B 151 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5594 Z= 0.398 Angle : 0.805 11.699 7580 Z= 0.426 Chirality : 0.048 0.235 808 Planarity : 0.005 0.030 962 Dihedral : 6.565 57.139 728 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.85 % Allowed : 24.25 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.45 (0.32), residues: 678 helix: -0.20 (0.68), residues: 68 sheet: -1.83 (0.39), residues: 158 loop : -1.86 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 311 HIS 0.007 0.001 HIS A 195 PHE 0.018 0.003 PHE A 217 TYR 0.019 0.002 TYR A 32 ARG 0.005 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 PHE cc_start: 0.8168 (m-80) cc_final: 0.7736 (m-80) REVERT: B 208 ASP cc_start: 0.8355 (p0) cc_final: 0.8132 (m-30) REVERT: B 232 TRP cc_start: 0.8746 (t60) cc_final: 0.8383 (t60) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.1654 time to fit residues: 21.9373 Evaluate side-chains 89 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 275 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5594 Z= 0.241 Angle : 0.742 11.712 7580 Z= 0.391 Chirality : 0.046 0.237 808 Planarity : 0.004 0.026 962 Dihedral : 6.026 56.882 727 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 6.19 % Allowed : 21.91 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.25 (0.33), residues: 678 helix: 0.11 (0.71), residues: 68 sheet: -1.81 (0.39), residues: 176 loop : -1.67 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 225 HIS 0.006 0.001 HIS B 195 PHE 0.010 0.002 PHE A 133 TYR 0.016 0.002 TYR A 32 ARG 0.004 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 81 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7316 (mmt90) REVERT: B 62 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7443 (ttt-90) REVERT: B 67 MET cc_start: 0.8983 (tmm) cc_final: 0.8764 (tmm) REVERT: B 232 TRP cc_start: 0.8685 (t60) cc_final: 0.8354 (t60) REVERT: B 322 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7443 (ptt90) outliers start: 37 outliers final: 21 residues processed: 103 average time/residue: 0.1639 time to fit residues: 22.2464 Evaluate side-chains 101 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 322 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5594 Z= 0.310 Angle : 0.758 11.797 7580 Z= 0.400 Chirality : 0.047 0.238 808 Planarity : 0.004 0.044 962 Dihedral : 6.080 49.108 727 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 6.35 % Allowed : 22.58 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.27 (0.33), residues: 678 helix: 0.09 (0.70), residues: 68 sheet: -1.71 (0.40), residues: 176 loop : -1.74 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 311 HIS 0.007 0.001 HIS B 195 PHE 0.014 0.002 PHE A 217 TYR 0.017 0.002 TYR A 32 ARG 0.012 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8510 (tmm) cc_final: 0.8009 (tmm) REVERT: A 272 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7341 (mmt90) REVERT: B 62 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7491 (ttt-90) REVERT: B 232 TRP cc_start: 0.8721 (t60) cc_final: 0.8431 (t60) REVERT: B 321 LEU cc_start: 0.9119 (tp) cc_final: 0.8894 (tp) REVERT: B 322 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7945 (ptt-90) outliers start: 38 outliers final: 24 residues processed: 98 average time/residue: 0.1540 time to fit residues: 20.3601 Evaluate side-chains 95 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 322 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.0570 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5594 Z= 0.165 Angle : 0.702 11.722 7580 Z= 0.369 Chirality : 0.046 0.239 808 Planarity : 0.004 0.028 962 Dihedral : 5.360 25.958 726 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.68 % Allowed : 24.58 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.04 (0.33), residues: 678 helix: 0.42 (0.71), residues: 68 sheet: -1.20 (0.43), residues: 144 loop : -1.79 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 225 HIS 0.004 0.001 HIS B 195 PHE 0.007 0.001 PHE A 133 TYR 0.016 0.001 TYR B 32 ARG 0.009 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8464 (tmm) cc_final: 0.7964 (tmm) REVERT: A 175 GLN cc_start: 0.8008 (pp30) cc_final: 0.7633 (pp30) REVERT: A 272 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7266 (mmt90) REVERT: B 34 PHE cc_start: 0.8334 (m-80) cc_final: 0.7750 (m-80) REVERT: B 62 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7362 (ttt-90) REVERT: B 67 MET cc_start: 0.9049 (tmm) cc_final: 0.8771 (tmm) REVERT: B 232 TRP cc_start: 0.8638 (t60) cc_final: 0.8279 (t60) REVERT: B 278 ASP cc_start: 0.7940 (m-30) cc_final: 0.7138 (m-30) outliers start: 28 outliers final: 16 residues processed: 101 average time/residue: 0.1580 time to fit residues: 21.5676 Evaluate side-chains 97 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5594 Z= 0.279 Angle : 0.729 11.762 7580 Z= 0.384 Chirality : 0.046 0.236 808 Planarity : 0.004 0.033 962 Dihedral : 5.545 27.503 726 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.52 % Allowed : 25.25 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.10 (0.33), residues: 678 helix: 0.43 (0.71), residues: 68 sheet: -1.61 (0.40), residues: 176 loop : -1.65 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.006 0.001 HIS B 195 PHE 0.013 0.002 PHE B 279 TYR 0.017 0.002 TYR B 32 ARG 0.008 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8499 (tmm) cc_final: 0.7962 (tmm) REVERT: A 175 GLN cc_start: 0.8076 (pp30) cc_final: 0.7785 (pp30) REVERT: A 272 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7376 (mmt90) REVERT: B 62 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7435 (ttt-90) REVERT: B 67 MET cc_start: 0.8953 (tmm) cc_final: 0.8727 (tmm) REVERT: B 183 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8233 (pp) REVERT: B 232 TRP cc_start: 0.8720 (t60) cc_final: 0.8420 (t60) outliers start: 27 outliers final: 19 residues processed: 88 average time/residue: 0.1590 time to fit residues: 18.7909 Evaluate side-chains 94 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5594 Z= 0.206 Angle : 0.717 11.721 7580 Z= 0.375 Chirality : 0.046 0.237 808 Planarity : 0.004 0.035 962 Dihedral : 5.426 26.776 726 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.68 % Allowed : 24.92 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.33), residues: 678 helix: 0.52 (0.71), residues: 68 sheet: -1.04 (0.45), residues: 142 loop : -1.78 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 225 HIS 0.004 0.001 HIS B 195 PHE 0.008 0.001 PHE A 217 TYR 0.017 0.001 TYR B 32 ARG 0.006 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8516 (tmm) cc_final: 0.8045 (tmm) REVERT: A 175 GLN cc_start: 0.8067 (pp30) cc_final: 0.7807 (pp30) REVERT: A 272 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7355 (mmt90) REVERT: B 62 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7389 (ttt-90) REVERT: B 67 MET cc_start: 0.9054 (tmm) cc_final: 0.8779 (tmm) REVERT: B 183 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 232 TRP cc_start: 0.8670 (t60) cc_final: 0.8364 (t60) outliers start: 28 outliers final: 20 residues processed: 92 average time/residue: 0.1626 time to fit residues: 20.0060 Evaluate side-chains 96 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5594 Z= 0.262 Angle : 0.731 11.750 7580 Z= 0.384 Chirality : 0.047 0.235 808 Planarity : 0.004 0.038 962 Dihedral : 5.546 27.585 726 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.01 % Allowed : 25.42 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.00 (0.33), residues: 678 helix: 0.49 (0.70), residues: 68 sheet: -1.45 (0.41), residues: 168 loop : -1.64 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 225 HIS 0.005 0.001 HIS B 195 PHE 0.012 0.002 PHE B 279 TYR 0.017 0.002 TYR B 32 ARG 0.007 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8527 (tmm) cc_final: 0.8072 (tmm) REVERT: A 175 GLN cc_start: 0.8038 (pp30) cc_final: 0.7749 (pp30) REVERT: A 198 MET cc_start: 0.8387 (mmm) cc_final: 0.7858 (mmt) REVERT: A 272 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7411 (mmt90) REVERT: B 62 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7434 (ttt-90) REVERT: B 67 MET cc_start: 0.9054 (tmm) cc_final: 0.8763 (tmm) REVERT: B 183 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8209 (pp) REVERT: B 232 TRP cc_start: 0.8745 (t60) cc_final: 0.8455 (t60) outliers start: 24 outliers final: 21 residues processed: 91 average time/residue: 0.1628 time to fit residues: 19.7421 Evaluate side-chains 97 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5594 Z= 0.176 Angle : 0.703 11.723 7580 Z= 0.368 Chirality : 0.046 0.235 808 Planarity : 0.003 0.037 962 Dihedral : 5.299 26.224 726 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.01 % Allowed : 26.25 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.33), residues: 678 helix: 0.67 (0.71), residues: 68 sheet: -0.96 (0.45), residues: 142 loop : -1.74 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 225 HIS 0.004 0.001 HIS B 195 PHE 0.008 0.001 PHE B 279 TYR 0.017 0.001 TYR B 32 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8459 (tmm) cc_final: 0.8014 (tmm) REVERT: A 175 GLN cc_start: 0.8037 (pp30) cc_final: 0.7785 (pp30) REVERT: A 272 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7358 (mmt90) REVERT: B 62 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7395 (ttt-90) REVERT: B 67 MET cc_start: 0.9065 (tmm) cc_final: 0.8792 (tmm) REVERT: B 183 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8301 (pp) REVERT: B 232 TRP cc_start: 0.8625 (t60) cc_final: 0.8303 (t60) outliers start: 18 outliers final: 12 residues processed: 90 average time/residue: 0.2284 time to fit residues: 27.7684 Evaluate side-chains 88 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 0.0070 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5594 Z= 0.235 Angle : 0.723 11.736 7580 Z= 0.379 Chirality : 0.046 0.235 808 Planarity : 0.004 0.039 962 Dihedral : 5.390 26.856 726 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.34 % Allowed : 25.75 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.34), residues: 678 helix: 0.58 (0.71), residues: 68 sheet: -1.12 (0.45), residues: 150 loop : -1.71 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 225 HIS 0.005 0.001 HIS B 195 PHE 0.011 0.001 PHE B 279 TYR 0.018 0.002 TYR A 323 ARG 0.006 0.000 ARG B 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8470 (tmm) cc_final: 0.8043 (tmm) REVERT: A 175 GLN cc_start: 0.8004 (pp30) cc_final: 0.7729 (pp30) REVERT: A 184 MET cc_start: 0.8140 (mtp) cc_final: 0.7824 (mtp) REVERT: A 272 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7337 (mmt90) REVERT: B 62 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7443 (ttt-90) REVERT: B 67 MET cc_start: 0.9064 (tmm) cc_final: 0.8776 (tmm) REVERT: B 183 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8197 (pp) REVERT: B 232 TRP cc_start: 0.8691 (t60) cc_final: 0.8391 (t60) outliers start: 20 outliers final: 15 residues processed: 85 average time/residue: 0.1702 time to fit residues: 19.3666 Evaluate side-chains 90 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.183946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134180 restraints weight = 7238.434| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.79 r_work: 0.3702 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5594 Z= 0.182 Angle : 0.708 11.730 7580 Z= 0.368 Chirality : 0.046 0.235 808 Planarity : 0.003 0.037 962 Dihedral : 5.273 26.078 726 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.34 % Allowed : 25.59 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.33), residues: 678 helix: 0.71 (0.72), residues: 68 sheet: -0.93 (0.45), residues: 142 loop : -1.69 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 225 HIS 0.004 0.001 HIS B 195 PHE 0.009 0.001 PHE B 279 TYR 0.017 0.001 TYR B 32 ARG 0.006 0.000 ARG B 324 =============================================================================== Job complete usr+sys time: 1474.57 seconds wall clock time: 27 minutes 25.15 seconds (1645.15 seconds total)