Starting phenix.real_space_refine on Fri Nov 15 11:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfj_60062/11_2024/8zfj_60062.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfj_60062/11_2024/8zfj_60062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfj_60062/11_2024/8zfj_60062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfj_60062/11_2024/8zfj_60062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfj_60062/11_2024/8zfj_60062.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zfj_60062/11_2024/8zfj_60062.cif" } resolution = 3.1 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= 0.082 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 55 5.16 5 C 5657 2.51 5 N 1541 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8903 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1764 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1938 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "R" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2141 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 3 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Time building chain proxies: 5.40, per 1000 atoms: 0.61 Number of scatterers: 8903 At special positions: 0 Unit cell: (84.63, 120.9, 125.55, 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 55 16.00 O 1650 8.00 N 1541 7.00 C 5657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 134 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 39.8% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 91 through 94 removed outlier: 3.933A pdb=" N GLY D 94 " --> pdb=" O SER D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 91 through 94' Processing helix chain 'D' and resid 125 through 129 removed outlier: 4.071A pdb=" N THR D 129 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.924A pdb=" N VAL D 262 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.828A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.795A pdb=" N GLN A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.972A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 336 removed outlier: 3.872A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing helix chain 'R' and resid 20 through 27 Processing helix chain 'R' and resid 30 through 56 Proline residue: R 41 - end of helix Processing helix chain 'R' and resid 59 through 89 removed outlier: 3.898A pdb=" N TYR R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 102 through 129 Processing helix chain 'R' and resid 138 through 163 Proline residue: R 160 - end of helix Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 198 through 218 removed outlier: 3.590A pdb=" N GLY R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 262 Proline residue: R 247 - end of helix Processing helix chain 'R' and resid 272 through 284 removed outlier: 3.827A pdb=" N SER R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 296 removed outlier: 3.877A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 298 through 315 Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.589A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.685A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.476A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.616A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.332A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.623A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.039A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.372A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.607A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 45 removed outlier: 3.587A pdb=" N PHE D 118 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER D 109 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.759A pdb=" N MET D 72 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR D 88 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP D 74 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 197 Processing sheet with id=AB2, first strand: chain 'D' and resid 224 through 227 removed outlier: 6.520A pdb=" N TRP D 214 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 57 through 58 removed outlier: 6.905A pdb=" N HIS A 34 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 215 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 36 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 217 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 38 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N ALA A 236 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 35 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE A 238 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 37 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 240 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 39 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASP A 242 " --> pdb=" O LEU A 39 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1353 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: 2.67 Time building geometry restraints manager: 2.81 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: 2906 1.34 - 1.46: 1875 1.46 - 1.58: 4234 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 9095 Sorted by residual: bond pdb=" CG PRO R 29 " pdb=" CD PRO R 29 " ideal model delta sigma weight residual 1.503 1.553 -0.050 3.40e-02 8.65e+02 2.20e+00 bond pdb=" CB GLU G 42 " pdb=" CG GLU G 42 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CG LEU B 55 " pdb=" CD2 LEU B 55 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 bond pdb=" CB PRO R 29 " pdb=" CG PRO R 29 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.22e+00 bond pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 1.535 1.549 -0.014 1.37e-02 5.33e+03 1.00e+00 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 11841 1.25 - 2.51: 368 2.51 - 3.76: 67 3.76 - 5.01: 42 5.01 - 6.26: 6 Bond angle restraints: 12324 Sorted by residual: angle pdb=" CA GLU G 42 " pdb=" CB GLU G 42 " pdb=" CG GLU G 42 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.81e+00 angle pdb=" CA PRO R 29 " pdb=" N PRO R 29 " pdb=" CD PRO R 29 " ideal model delta sigma weight residual 112.00 108.15 3.85 1.40e+00 5.10e-01 7.58e+00 angle pdb=" CB GLU G 42 " pdb=" CG GLU G 42 " pdb=" CD GLU G 42 " ideal model delta sigma weight residual 112.60 117.24 -4.64 1.70e+00 3.46e-01 7.46e+00 angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 109.85 3.80 1.47e+00 4.63e-01 6.69e+00 angle pdb=" CA GLN R 28 " pdb=" CB GLN R 28 " pdb=" CG GLN R 28 " ideal model delta sigma weight residual 114.10 119.17 -5.07 2.00e+00 2.50e-01 6.42e+00 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4519 17.09 - 34.18: 649 34.18 - 51.27: 177 51.27 - 68.36: 30 68.36 - 85.45: 7 Dihedral angle restraints: 5382 sinusoidal: 2104 harmonic: 3278 Sorted by residual: dihedral pdb=" CB CYS D 60 " pdb=" SG CYS D 60 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual 93.00 29.55 63.45 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA PRO D 145 " pdb=" C PRO D 145 " pdb=" N PHE D 146 " pdb=" CA PHE D 146 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 903 0.034 - 0.069: 318 0.069 - 0.103: 114 0.103 - 0.137: 41 0.137 - 0.172: 2 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA TYR D 273 " pdb=" N TYR D 273 " pdb=" C TYR D 273 " pdb=" CB TYR D 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1375 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 28 " -0.045 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO R 29 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO R 29 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 29 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 218 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO D 219 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 219 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 219 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C THR B 87 " 0.034 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.011 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 238 2.69 - 3.24: 8743 3.24 - 3.79: 14820 3.79 - 4.35: 19385 4.35 - 4.90: 32373 Nonbonded interactions: 75559 Sorted by model distance: nonbonded pdb=" OH TYR D 213 " pdb=" OE2 GLU A 8 " model vdw 2.131 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.142 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.149 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.197 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.198 3.040 ... (remaining 75554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.700 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 0.055 9095 Z= 0.229 Angle : 0.578 6.263 12324 Z= 0.306 Chirality : 0.043 0.172 1378 Planarity : 0.005 0.066 1571 Dihedral : 16.992 85.447 3269 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.62 % Allowed : 28.33 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1112 helix: 1.96 (0.26), residues: 402 sheet: -0.01 (0.32), residues: 274 loop : -0.50 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 48 HIS 0.003 0.001 HIS A 340 PHE 0.018 0.001 PHE R 27 TYR 0.020 0.001 TYR A 322 ARG 0.007 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.996 Fit side-chains REVERT: B 17 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6633 (tt0) REVERT: B 129 ARG cc_start: 0.7570 (ttt90) cc_final: 0.7334 (ttt90) REVERT: D 214 TRP cc_start: 0.6926 (m100) cc_final: 0.6533 (m100) REVERT: A 292 GLU cc_start: 0.8173 (mp0) cc_final: 0.7913 (mp0) REVERT: A 339 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6575 (mmp80) REVERT: R 154 ILE cc_start: 0.7805 (mm) cc_final: 0.7449 (mt) REVERT: R 205 MET cc_start: 0.8120 (ttm) cc_final: 0.7807 (ttt) outliers start: 6 outliers final: 1 residues processed: 174 average time/residue: 0.2501 time to fit residues: 58.5309 Evaluate side-chains 151 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 221 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9095 Z= 0.219 Angle : 0.578 7.398 12324 Z= 0.305 Chirality : 0.044 0.160 1378 Planarity : 0.004 0.049 1571 Dihedral : 4.250 28.559 1238 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.06 % Allowed : 24.58 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1112 helix: 2.17 (0.25), residues: 413 sheet: -0.00 (0.33), residues: 262 loop : -0.57 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 249 PHE 0.014 0.001 PHE R 27 TYR 0.020 0.002 TYR A 322 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.881 Fit side-chains REVERT: B 17 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6589 (tt0) REVERT: B 198 LEU cc_start: 0.8293 (mt) cc_final: 0.7984 (mt) REVERT: D 149 TRP cc_start: 0.8098 (m100) cc_final: 0.7825 (m100) REVERT: A 204 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7417 (mmtp) REVERT: A 224 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.6672 (ttm-80) REVERT: A 245 ASP cc_start: 0.7497 (t0) cc_final: 0.7187 (t0) REVERT: A 247 ASN cc_start: 0.8238 (m-40) cc_final: 0.7735 (m-40) REVERT: A 292 GLU cc_start: 0.8152 (mp0) cc_final: 0.7800 (mp0) REVERT: A 361 ASP cc_start: 0.8640 (m-30) cc_final: 0.8293 (m-30) REVERT: R 135 LYS cc_start: 0.6666 (pttp) cc_final: 0.5893 (tttm) REVERT: G 62 ARG cc_start: 0.6715 (ptp90) cc_final: 0.6194 (ptp90) outliers start: 39 outliers final: 26 residues processed: 179 average time/residue: 0.2158 time to fit residues: 52.7240 Evaluate side-chains 162 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.0040 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN R 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9095 Z= 0.192 Angle : 0.535 6.973 12324 Z= 0.282 Chirality : 0.043 0.202 1378 Planarity : 0.004 0.047 1571 Dihedral : 4.092 27.577 1237 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.17 % Allowed : 24.69 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1112 helix: 2.33 (0.25), residues: 413 sheet: 0.04 (0.34), residues: 261 loop : -0.53 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS A 340 PHE 0.012 0.001 PHE D 67 TYR 0.016 0.001 TYR A 322 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6620 (tt0) REVERT: A 39 LEU cc_start: 0.8395 (mt) cc_final: 0.8192 (mt) REVERT: A 204 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7563 (mmtp) REVERT: A 245 ASP cc_start: 0.7396 (t0) cc_final: 0.6978 (t0) REVERT: A 247 ASN cc_start: 0.8402 (m-40) cc_final: 0.7900 (m-40) REVERT: A 292 GLU cc_start: 0.8244 (mp0) cc_final: 0.7818 (mp0) REVERT: A 353 GLU cc_start: 0.7655 (pm20) cc_final: 0.7385 (pm20) REVERT: R 52 MET cc_start: 0.7113 (mmp) cc_final: 0.6773 (mmp) REVERT: R 135 LYS cc_start: 0.6737 (pttp) cc_final: 0.5948 (tttm) REVERT: R 195 PHE cc_start: 0.7362 (t80) cc_final: 0.6732 (t80) REVERT: R 217 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7355 (mtm110) REVERT: R 226 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7597 (mt-10) REVERT: G 62 ARG cc_start: 0.6721 (ptp90) cc_final: 0.6187 (ptp90) outliers start: 40 outliers final: 32 residues processed: 188 average time/residue: 0.2139 time to fit residues: 55.8265 Evaluate side-chains 170 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 288 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 221 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN R 298 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9095 Z= 0.222 Angle : 0.549 7.062 12324 Z= 0.287 Chirality : 0.043 0.175 1378 Planarity : 0.004 0.047 1571 Dihedral : 4.105 28.073 1237 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.00 % Allowed : 23.54 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1112 helix: 2.27 (0.25), residues: 413 sheet: -0.15 (0.33), residues: 266 loop : -0.52 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS A 340 PHE 0.031 0.002 PHE R 259 TYR 0.017 0.001 TYR A 322 ARG 0.012 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.391 Fit side-chains REVERT: B 17 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6599 (tt0) REVERT: B 59 TYR cc_start: 0.8239 (m-80) cc_final: 0.7932 (m-80) REVERT: A 204 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7730 (mmtt) REVERT: A 245 ASP cc_start: 0.7351 (t0) cc_final: 0.6903 (t0) REVERT: A 247 ASN cc_start: 0.8492 (m-40) cc_final: 0.8010 (m-40) REVERT: A 292 GLU cc_start: 0.8338 (mp0) cc_final: 0.7908 (mp0) REVERT: A 301 TYR cc_start: 0.7551 (t80) cc_final: 0.6905 (t80) REVERT: A 326 ASP cc_start: 0.7737 (m-30) cc_final: 0.6938 (m-30) REVERT: A 339 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6521 (mmp80) REVERT: A 353 GLU cc_start: 0.7833 (pm20) cc_final: 0.7364 (pm20) REVERT: R 52 MET cc_start: 0.7184 (mmp) cc_final: 0.6859 (mmp) REVERT: R 135 LYS cc_start: 0.6752 (pttp) cc_final: 0.5999 (tttm) REVERT: R 195 PHE cc_start: 0.7556 (t80) cc_final: 0.7297 (t80) REVERT: R 217 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7389 (mtm110) REVERT: R 226 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7490 (mt-10) REVERT: G 62 ARG cc_start: 0.6755 (ptp90) cc_final: 0.6238 (ptp90) outliers start: 48 outliers final: 33 residues processed: 192 average time/residue: 0.2365 time to fit residues: 62.6381 Evaluate side-chains 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 288 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 ASN ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9095 Z= 0.187 Angle : 0.536 6.782 12324 Z= 0.279 Chirality : 0.042 0.155 1378 Planarity : 0.004 0.049 1571 Dihedral : 4.023 27.634 1237 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.17 % Allowed : 24.38 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1112 helix: 2.31 (0.25), residues: 414 sheet: -0.07 (0.33), residues: 265 loop : -0.49 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 340 PHE 0.019 0.001 PHE R 259 TYR 0.016 0.001 TYR A 322 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7131 (tm-30) cc_final: 0.6604 (tt0) REVERT: B 74 SER cc_start: 0.8587 (p) cc_final: 0.8350 (p) REVERT: B 130 GLU cc_start: 0.7961 (mp0) cc_final: 0.7553 (mp0) REVERT: A 204 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7714 (mmtt) REVERT: A 245 ASP cc_start: 0.7239 (t0) cc_final: 0.6854 (t0) REVERT: A 247 ASN cc_start: 0.8498 (m-40) cc_final: 0.8031 (m-40) REVERT: A 292 GLU cc_start: 0.8365 (mp0) cc_final: 0.7929 (mp0) REVERT: A 297 GLU cc_start: 0.7587 (mp0) cc_final: 0.6880 (tp30) REVERT: A 326 ASP cc_start: 0.7775 (m-30) cc_final: 0.6974 (m-30) REVERT: R 52 MET cc_start: 0.7158 (mmp) cc_final: 0.6801 (mmp) REVERT: R 135 LYS cc_start: 0.6641 (pttp) cc_final: 0.5892 (tttm) REVERT: R 226 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7534 (mt-10) REVERT: R 277 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6452 (m-70) REVERT: G 62 ARG cc_start: 0.6753 (ptp90) cc_final: 0.6277 (ptp90) outliers start: 40 outliers final: 31 residues processed: 183 average time/residue: 0.2102 time to fit residues: 53.5614 Evaluate side-chains 173 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 HIS R 277 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9095 Z= 0.299 Angle : 0.591 7.617 12324 Z= 0.306 Chirality : 0.044 0.166 1378 Planarity : 0.004 0.049 1571 Dihedral : 4.259 28.460 1237 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.85 % Allowed : 24.69 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1112 helix: 2.17 (0.25), residues: 413 sheet: -0.08 (0.34), residues: 264 loop : -0.57 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.005 0.001 HIS A 340 PHE 0.021 0.002 PHE R 259 TYR 0.018 0.002 TYR A 322 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.115 Fit side-chains REVERT: B 17 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6634 (tt0) REVERT: A 54 ARG cc_start: 0.6369 (mmt90) cc_final: 0.5988 (mmt90) REVERT: A 209 LYS cc_start: 0.8103 (mptt) cc_final: 0.7492 (mmmt) REVERT: A 245 ASP cc_start: 0.7247 (t0) cc_final: 0.6807 (t0) REVERT: A 247 ASN cc_start: 0.8608 (m-40) cc_final: 0.8140 (m-40) REVERT: A 292 GLU cc_start: 0.8434 (mp0) cc_final: 0.8131 (mp0) REVERT: R 52 MET cc_start: 0.7338 (mmp) cc_final: 0.7074 (mmp) REVERT: R 135 LYS cc_start: 0.6579 (pttp) cc_final: 0.5863 (tttm) REVERT: R 205 MET cc_start: 0.8263 (ttm) cc_final: 0.8061 (ttm) REVERT: R 226 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7534 (mt-10) REVERT: G 62 ARG cc_start: 0.6846 (ptp90) cc_final: 0.6304 (ptp90) outliers start: 37 outliers final: 31 residues processed: 165 average time/residue: 0.2298 time to fit residues: 51.3313 Evaluate side-chains 165 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 232 ASN R 108 ASN R 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9095 Z= 0.229 Angle : 0.563 7.572 12324 Z= 0.289 Chirality : 0.043 0.159 1378 Planarity : 0.004 0.050 1571 Dihedral : 4.158 27.833 1237 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.17 % Allowed : 24.58 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1112 helix: 2.23 (0.25), residues: 413 sheet: -0.04 (0.34), residues: 262 loop : -0.53 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 340 PHE 0.018 0.001 PHE R 259 TYR 0.016 0.001 TYR A 322 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.979 Fit side-chains REVERT: B 17 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6691 (tt0) REVERT: B 130 GLU cc_start: 0.8020 (mp0) cc_final: 0.7624 (mp0) REVERT: B 153 ASP cc_start: 0.7965 (p0) cc_final: 0.7692 (p0) REVERT: A 54 ARG cc_start: 0.6235 (mmt90) cc_final: 0.5853 (mmt90) REVERT: A 209 LYS cc_start: 0.8106 (mptt) cc_final: 0.7495 (mmmt) REVERT: A 245 ASP cc_start: 0.7201 (t0) cc_final: 0.6774 (t0) REVERT: A 247 ASN cc_start: 0.8583 (m-40) cc_final: 0.8134 (m-40) REVERT: A 292 GLU cc_start: 0.8490 (mp0) cc_final: 0.8007 (mp0) REVERT: A 297 GLU cc_start: 0.7601 (mp0) cc_final: 0.7323 (mp0) REVERT: R 52 MET cc_start: 0.7306 (mmp) cc_final: 0.7046 (mmp) REVERT: R 135 LYS cc_start: 0.6611 (pttp) cc_final: 0.5950 (tttm) REVERT: R 226 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7548 (mt-10) REVERT: G 62 ARG cc_start: 0.6869 (ptp90) cc_final: 0.6365 (ptp90) outliers start: 40 outliers final: 35 residues processed: 168 average time/residue: 0.2226 time to fit residues: 51.3091 Evaluate side-chains 167 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 288 VAL Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 40.0000 chunk 99 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN R 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9095 Z= 0.206 Angle : 0.554 6.798 12324 Z= 0.285 Chirality : 0.043 0.154 1378 Planarity : 0.004 0.050 1571 Dihedral : 4.120 27.624 1237 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.54 % Allowed : 25.94 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1112 helix: 2.32 (0.25), residues: 409 sheet: -0.06 (0.34), residues: 262 loop : -0.48 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 340 PHE 0.017 0.001 PHE R 259 TYR 0.015 0.001 TYR A 322 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.937 Fit side-chains REVERT: B 17 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6690 (tt0) REVERT: B 74 SER cc_start: 0.8780 (p) cc_final: 0.8575 (p) REVERT: B 130 GLU cc_start: 0.8005 (mp0) cc_final: 0.7596 (mp0) REVERT: B 214 ARG cc_start: 0.7478 (mmt90) cc_final: 0.7250 (mmt180) REVERT: D 89 ILE cc_start: 0.8133 (tt) cc_final: 0.7897 (tt) REVERT: A 54 ARG cc_start: 0.6277 (mmt90) cc_final: 0.5831 (mmt90) REVERT: A 209 LYS cc_start: 0.8041 (mptt) cc_final: 0.7458 (mmmt) REVERT: A 224 ARG cc_start: 0.7896 (ptp-170) cc_final: 0.7416 (ptp-170) REVERT: A 245 ASP cc_start: 0.7149 (t0) cc_final: 0.6744 (t0) REVERT: A 247 ASN cc_start: 0.8588 (m-40) cc_final: 0.8151 (m-40) REVERT: A 292 GLU cc_start: 0.8503 (mp0) cc_final: 0.8013 (mp0) REVERT: A 297 GLU cc_start: 0.7543 (mp0) cc_final: 0.7272 (mp0) REVERT: R 52 MET cc_start: 0.7288 (mmp) cc_final: 0.7017 (mmp) REVERT: R 135 LYS cc_start: 0.6601 (pttp) cc_final: 0.5941 (tttm) REVERT: R 226 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7567 (mt-10) REVERT: G 62 ARG cc_start: 0.6856 (ptp90) cc_final: 0.6211 (ptp90) outliers start: 34 outliers final: 31 residues processed: 159 average time/residue: 0.2325 time to fit residues: 50.6442 Evaluate side-chains 158 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9095 Z= 0.230 Angle : 0.569 7.824 12324 Z= 0.295 Chirality : 0.043 0.159 1378 Planarity : 0.004 0.050 1571 Dihedral : 4.136 27.599 1237 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.75 % Allowed : 25.62 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1112 helix: 2.32 (0.25), residues: 409 sheet: -0.00 (0.34), residues: 259 loop : -0.43 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS A 340 PHE 0.016 0.001 PHE R 259 TYR 0.016 0.001 TYR A 322 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.947 Fit side-chains REVERT: B 17 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6831 (tt0) REVERT: B 214 ARG cc_start: 0.7505 (mmt90) cc_final: 0.7251 (mmt180) REVERT: D 89 ILE cc_start: 0.8211 (tt) cc_final: 0.7981 (tt) REVERT: A 54 ARG cc_start: 0.6249 (mmt90) cc_final: 0.5948 (mmt90) REVERT: A 209 LYS cc_start: 0.8048 (mptt) cc_final: 0.7473 (mmmt) REVERT: A 224 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7361 (ptp-170) REVERT: A 245 ASP cc_start: 0.7272 (t0) cc_final: 0.6841 (t0) REVERT: A 247 ASN cc_start: 0.8607 (m-40) cc_final: 0.8182 (m-40) REVERT: A 292 GLU cc_start: 0.8527 (mp0) cc_final: 0.8043 (mp0) REVERT: A 297 GLU cc_start: 0.7537 (mp0) cc_final: 0.7272 (mp0) REVERT: R 52 MET cc_start: 0.7303 (mmp) cc_final: 0.7033 (mmp) REVERT: R 135 LYS cc_start: 0.6646 (pttp) cc_final: 0.5962 (tttm) REVERT: R 205 MET cc_start: 0.8301 (ttm) cc_final: 0.8085 (ttm) REVERT: R 226 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7540 (mt-10) REVERT: G 62 ARG cc_start: 0.6853 (ptp90) cc_final: 0.6215 (ptp90) outliers start: 36 outliers final: 34 residues processed: 157 average time/residue: 0.2219 time to fit residues: 47.9848 Evaluate side-chains 160 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 288 VAL Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9095 Z= 0.229 Angle : 0.566 7.072 12324 Z= 0.292 Chirality : 0.043 0.157 1378 Planarity : 0.004 0.050 1571 Dihedral : 4.135 27.516 1237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.54 % Allowed : 25.94 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1112 helix: 2.33 (0.25), residues: 409 sheet: -0.06 (0.33), residues: 262 loop : -0.43 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 340 PHE 0.015 0.001 PHE R 259 TYR 0.016 0.001 TYR A 322 ARG 0.004 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.981 Fit side-chains REVERT: B 17 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6801 (tt0) REVERT: B 46 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7290 (ttm-80) REVERT: B 130 GLU cc_start: 0.8042 (mp0) cc_final: 0.7639 (mp0) REVERT: B 214 ARG cc_start: 0.7529 (mmt90) cc_final: 0.7276 (mmt180) REVERT: D 89 ILE cc_start: 0.8229 (tt) cc_final: 0.8004 (tt) REVERT: A 54 ARG cc_start: 0.6229 (mmt90) cc_final: 0.5931 (mmt90) REVERT: A 209 LYS cc_start: 0.8067 (mptt) cc_final: 0.7480 (mmmt) REVERT: A 224 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7506 (ptp-170) REVERT: A 245 ASP cc_start: 0.7268 (t0) cc_final: 0.6803 (t0) REVERT: A 247 ASN cc_start: 0.8620 (m-40) cc_final: 0.8206 (m110) REVERT: A 292 GLU cc_start: 0.8541 (mp0) cc_final: 0.8059 (mp0) REVERT: A 297 GLU cc_start: 0.7601 (mp0) cc_final: 0.7356 (mp0) REVERT: A 322 TYR cc_start: 0.8173 (m-80) cc_final: 0.7957 (m-80) REVERT: R 52 MET cc_start: 0.7300 (mmp) cc_final: 0.7030 (mmp) REVERT: R 135 LYS cc_start: 0.6639 (pttp) cc_final: 0.5956 (tttm) REVERT: R 226 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7540 (mt-10) REVERT: G 62 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6222 (ptp90) outliers start: 34 outliers final: 34 residues processed: 154 average time/residue: 0.2254 time to fit residues: 48.2478 Evaluate side-chains 160 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 288 VAL Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN D 77 GLN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.186429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150232 restraints weight = 9724.702| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.30 r_work: 0.3271 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9095 Z= 0.190 Angle : 0.546 7.028 12324 Z= 0.282 Chirality : 0.042 0.152 1378 Planarity : 0.004 0.050 1571 Dihedral : 4.067 27.485 1237 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.65 % Allowed : 25.94 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1112 helix: 2.39 (0.25), residues: 409 sheet: -0.00 (0.33), residues: 261 loop : -0.39 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 340 PHE 0.015 0.001 PHE R 259 TYR 0.015 0.001 TYR A 322 ARG 0.004 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.86 seconds wall clock time: 40 minutes 36.24 seconds (2436.24 seconds total)