Starting phenix.real_space_refine on Mon Mar 11 03:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysn_34077/03_2024/7ysn_34077_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysn_34077/03_2024/7ysn_34077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysn_34077/03_2024/7ysn_34077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysn_34077/03_2024/7ysn_34077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysn_34077/03_2024/7ysn_34077_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysn_34077/03_2024/7ysn_34077_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 48 5.16 5 C 4296 2.51 5 N 1167 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6844 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3404 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3376 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.19, per 1000 atoms: 0.61 Number of scatterers: 6844 At special positions: 0 Unit cell: (112.136, 70.192, 69.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 6 15.00 O 1327 8.00 N 1167 7.00 C 4296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 6 sheets defined 44.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 72 through 79 removed outlier: 3.669A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.954A pdb=" N ILE A 115 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 128 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.330A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.961A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.540A pdb=" N ASP A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS A 401 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.786A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.524A pdb=" N ARG B 79 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.142A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 Processing helix chain 'B' and resid 181 through 196 Proline residue: B 184 - end of helix removed outlier: 3.593A pdb=" N GLU B 196 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.578A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.842A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 437 Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.492A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 65 through 68 removed outlier: 9.132A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'B' and resid 269 through 273 274 hydrogen bonds defined for protein. 651 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: 1.78 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2285 1.35 - 1.48: 1715 1.48 - 1.61: 2913 1.61 - 1.73: 9 1.73 - 1.86: 78 Bond restraints: 7000 Sorted by residual: bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.298 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C6 G2P B 501 " pdb=" O6 G2P B 501 " ideal model delta sigma weight residual 1.223 1.400 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C1' G2P B 501 " pdb=" O4' G2P B 501 " ideal model delta sigma weight residual 1.389 1.548 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C4' G2P B 501 " pdb=" O4' G2P B 501 " ideal model delta sigma weight residual 1.426 1.300 0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " ideal model delta sigma weight residual 1.448 1.333 0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 6995 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.98: 229 106.98 - 114.28: 3964 114.28 - 121.58: 3752 121.58 - 128.89: 1518 128.89 - 136.19: 46 Bond angle restraints: 9509 Sorted by residual: angle pdb=" N VAL A 182 " pdb=" CA VAL A 182 " pdb=" C VAL A 182 " ideal model delta sigma weight residual 112.29 107.82 4.47 9.40e-01 1.13e+00 2.26e+01 angle pdb=" N GLU A 420 " pdb=" CA GLU A 420 " pdb=" CB GLU A 420 " ideal model delta sigma weight residual 110.28 116.26 -5.98 1.55e+00 4.16e-01 1.49e+01 angle pdb=" C LYS B 124 " pdb=" N GLU B 125 " pdb=" CA GLU B 125 " ideal model delta sigma weight residual 121.14 114.89 6.25 1.75e+00 3.27e-01 1.27e+01 angle pdb=" C3A G2P B 501 " pdb=" PA G2P B 501 " pdb=" O5' G2P B 501 " ideal model delta sigma weight residual 99.14 109.76 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " pdb=" O3B G2P B 501 " ideal model delta sigma weight residual 99.71 109.83 -10.12 3.00e+00 1.11e-01 1.14e+01 ... (remaining 9504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 4022 28.12 - 56.23: 143 56.23 - 84.35: 17 84.35 - 112.46: 1 112.46 - 140.58: 2 Dihedral angle restraints: 4185 sinusoidal: 1688 harmonic: 2497 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -35.98 140.58 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -176.82 -113.91 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" CA ALA B 304 " pdb=" C ALA B 304 " pdb=" N CYS B 305 " pdb=" CA CYS B 305 " ideal model delta harmonic sigma weight residual 180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 785 0.049 - 0.098: 208 0.098 - 0.147: 43 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU A 420 " pdb=" N GLU A 420 " pdb=" C GLU A 420 " pdb=" CB GLU A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA GLU A 183 " pdb=" N GLU A 183 " pdb=" C GLU A 183 " pdb=" CB GLU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 1036 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 407 " 0.011 2.00e-02 2.50e+03 9.53e-03 2.27e+00 pdb=" CG TRP B 407 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 407 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 407 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 407 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 407 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 407 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 407 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 407 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 407 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 32 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 325 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.019 5.00e-02 4.00e+02 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 204 2.69 - 3.24: 7322 3.24 - 3.79: 11972 3.79 - 4.35: 15369 4.35 - 4.90: 24883 Nonbonded interactions: 59750 Sorted by model distance: nonbonded pdb=" O GLY A 416 " pdb=" OG SER A 419 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR B 185 " pdb=" O MET B 398 " model vdw 2.186 2.440 nonbonded pdb=" O LEU B 194 " pdb=" OG1 THR B 198 " model vdw 2.212 2.440 nonbonded pdb=" OG SER B 25 " pdb=" OH TYR B 53 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 292 " pdb=" OH TYR A 319 " model vdw 2.257 2.440 ... (remaining 59745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 1.620 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.430 Find NCS groups from input model: 0.190 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.006 0.230 7000 Z= 0.383 Angle : 0.693 10.618 9509 Z= 0.330 Chirality : 0.045 0.245 1039 Planarity : 0.003 0.036 1238 Dihedral : 14.723 140.575 2583 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 858 helix: 0.98 (0.26), residues: 382 sheet: -0.16 (0.50), residues: 125 loop : -0.37 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 407 HIS 0.003 0.001 HIS B 406 PHE 0.009 0.001 PHE B 388 TYR 0.014 0.001 TYR A 432 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9158 (t0) cc_final: 0.8905 (t0) REVERT: A 153 LEU cc_start: 0.9594 (tp) cc_final: 0.9393 (tp) REVERT: A 157 LEU cc_start: 0.9565 (mt) cc_final: 0.9299 (mt) REVERT: A 377 MET cc_start: 0.8810 (tmm) cc_final: 0.8608 (tmm) REVERT: A 386 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 398 MET cc_start: 0.7572 (tpt) cc_final: 0.7369 (tpt) REVERT: A 420 GLU cc_start: 0.8501 (pm20) cc_final: 0.8066 (pm20) REVERT: B 70 LEU cc_start: 0.8505 (mm) cc_final: 0.8268 (mm) REVERT: B 75 MET cc_start: 0.9112 (ttt) cc_final: 0.8605 (ttm) REVERT: B 79 ARG cc_start: 0.8805 (mpp80) cc_final: 0.8288 (mpt-90) REVERT: B 86 ILE cc_start: 0.8807 (pt) cc_final: 0.8538 (pt) REVERT: B 105 LYS cc_start: 0.8988 (tptp) cc_final: 0.8674 (tppt) REVERT: B 108 TYR cc_start: 0.8359 (m-10) cc_final: 0.8033 (m-10) REVERT: B 137 LEU cc_start: 0.9413 (tp) cc_final: 0.9171 (tp) REVERT: B 156 LYS cc_start: 0.9673 (mmpt) cc_final: 0.9453 (mmmt) REVERT: B 196 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8459 (mm-30) REVERT: B 398 MET cc_start: 0.8391 (mmp) cc_final: 0.7955 (mmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1680 time to fit residues: 35.8167 Evaluate side-chains 128 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7000 Z= 0.253 Angle : 0.621 6.783 9509 Z= 0.324 Chirality : 0.045 0.198 1039 Planarity : 0.005 0.038 1238 Dihedral : 8.758 136.637 984 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.36 % Allowed : 9.63 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.14 (0.29), residues: 858 helix: 0.67 (0.26), residues: 373 sheet: -0.05 (0.49), residues: 133 loop : -0.33 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 407 HIS 0.005 0.001 HIS B 192 PHE 0.011 0.001 PHE B 388 TYR 0.011 0.001 TYR A 408 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.847 Fit side-chains REVERT: A 24 TYR cc_start: 0.8253 (m-10) cc_final: 0.7508 (m-80) REVERT: A 102 ASN cc_start: 0.9288 (t0) cc_final: 0.8901 (t0) REVERT: A 153 LEU cc_start: 0.9641 (tp) cc_final: 0.9394 (tp) REVERT: A 157 LEU cc_start: 0.9580 (mt) cc_final: 0.9305 (mt) REVERT: A 377 MET cc_start: 0.8677 (tmm) cc_final: 0.8250 (tmm) REVERT: A 386 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8646 (mp0) REVERT: A 398 MET cc_start: 0.7982 (tpt) cc_final: 0.7594 (tpt) REVERT: A 420 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: B 21 TRP cc_start: 0.8998 (m100) cc_final: 0.8780 (m100) REVERT: B 70 LEU cc_start: 0.8578 (mm) cc_final: 0.8289 (mm) REVERT: B 75 MET cc_start: 0.9201 (ttt) cc_final: 0.8469 (ttp) REVERT: B 79 ARG cc_start: 0.8939 (mpp80) cc_final: 0.8115 (mpt-90) REVERT: B 86 ILE cc_start: 0.8688 (pt) cc_final: 0.8291 (tp) REVERT: B 103 TRP cc_start: 0.7099 (t60) cc_final: 0.6180 (t60) REVERT: B 105 LYS cc_start: 0.9013 (tptp) cc_final: 0.8664 (tppt) REVERT: B 137 LEU cc_start: 0.9398 (tp) cc_final: 0.9142 (tp) REVERT: B 153 LEU cc_start: 0.9438 (mt) cc_final: 0.9197 (mt) REVERT: B 156 LYS cc_start: 0.9677 (mmpt) cc_final: 0.9429 (mmmt) REVERT: B 196 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8407 (mm-30) REVERT: B 259 MET cc_start: 0.8774 (mmm) cc_final: 0.8414 (mmm) REVERT: B 325 MET cc_start: 0.8337 (ttm) cc_final: 0.8115 (ttm) REVERT: B 417 GLU cc_start: 0.8648 (mp0) cc_final: 0.8360 (mp0) outliers start: 10 outliers final: 6 residues processed: 141 average time/residue: 0.1685 time to fit residues: 32.9240 Evaluate side-chains 132 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 214 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7000 Z= 0.208 Angle : 0.605 7.917 9509 Z= 0.310 Chirality : 0.045 0.167 1039 Planarity : 0.004 0.039 1238 Dihedral : 8.791 138.209 984 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.76 % Allowed : 13.30 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 858 helix: 0.45 (0.27), residues: 375 sheet: -0.11 (0.49), residues: 128 loop : -0.32 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 407 HIS 0.004 0.001 HIS B 192 PHE 0.014 0.001 PHE B 319 TYR 0.011 0.001 TYR A 210 ARG 0.004 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8163 (m-10) cc_final: 0.7450 (m-80) REVERT: A 102 ASN cc_start: 0.9261 (t0) cc_final: 0.8890 (t0) REVERT: A 153 LEU cc_start: 0.9651 (tp) cc_final: 0.9397 (tp) REVERT: A 157 LEU cc_start: 0.9565 (mt) cc_final: 0.9290 (mt) REVERT: A 377 MET cc_start: 0.8662 (tmm) cc_final: 0.8191 (tmm) REVERT: A 386 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8660 (mp0) REVERT: A 398 MET cc_start: 0.8048 (tpt) cc_final: 0.7663 (tpt) REVERT: A 420 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: B 70 LEU cc_start: 0.8517 (mm) cc_final: 0.8268 (mm) REVERT: B 75 MET cc_start: 0.9182 (ttt) cc_final: 0.8508 (ttp) REVERT: B 79 ARG cc_start: 0.8913 (mpp80) cc_final: 0.8092 (mpt-90) REVERT: B 105 LYS cc_start: 0.8976 (tptp) cc_final: 0.8436 (tppt) REVERT: B 156 LYS cc_start: 0.9674 (mmpt) cc_final: 0.9434 (mmmt) REVERT: B 196 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8396 (mm-30) REVERT: B 417 GLU cc_start: 0.8733 (mp0) cc_final: 0.8394 (mp0) outliers start: 13 outliers final: 7 residues processed: 141 average time/residue: 0.1568 time to fit residues: 31.1866 Evaluate side-chains 136 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 214 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 52 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7000 Z= 0.258 Angle : 0.630 8.561 9509 Z= 0.327 Chirality : 0.045 0.171 1039 Planarity : 0.005 0.039 1238 Dihedral : 8.964 140.842 984 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.63 % Allowed : 15.74 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.26 (0.29), residues: 858 helix: 0.31 (0.27), residues: 368 sheet: -0.32 (0.48), residues: 128 loop : -0.45 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 407 HIS 0.010 0.001 HIS B 406 PHE 0.015 0.001 PHE B 319 TYR 0.014 0.001 TYR B 108 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.922 Fit side-chains REVERT: A 24 TYR cc_start: 0.8220 (m-10) cc_final: 0.7447 (m-80) REVERT: A 102 ASN cc_start: 0.9262 (t0) cc_final: 0.8923 (t0) REVERT: A 153 LEU cc_start: 0.9665 (tp) cc_final: 0.9417 (tp) REVERT: A 157 LEU cc_start: 0.9569 (mt) cc_final: 0.9307 (mt) REVERT: A 377 MET cc_start: 0.8670 (tmm) cc_final: 0.8189 (tmm) REVERT: A 386 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 398 MET cc_start: 0.8161 (tpt) cc_final: 0.7701 (tpt) REVERT: A 420 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: B 70 LEU cc_start: 0.8533 (mm) cc_final: 0.8312 (mm) REVERT: B 75 MET cc_start: 0.9180 (ttt) cc_final: 0.8580 (ttp) REVERT: B 79 ARG cc_start: 0.8865 (mpp80) cc_final: 0.8082 (mpt-90) REVERT: B 105 LYS cc_start: 0.8969 (tptp) cc_final: 0.8534 (tppt) REVERT: B 108 TYR cc_start: 0.8060 (m-80) cc_final: 0.7681 (m-80) REVERT: B 156 LYS cc_start: 0.9680 (mmpt) cc_final: 0.9429 (mmmt) REVERT: B 166 MET cc_start: 0.8947 (tpp) cc_final: 0.8316 (ttp) REVERT: B 196 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8402 (mm-30) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.1588 time to fit residues: 31.2198 Evaluate side-chains 130 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 214 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7000 Z= 0.208 Angle : 0.627 8.263 9509 Z= 0.320 Chirality : 0.044 0.170 1039 Planarity : 0.004 0.039 1238 Dihedral : 8.932 140.694 984 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.76 % Allowed : 17.91 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.25 (0.29), residues: 858 helix: 0.26 (0.27), residues: 368 sheet: -0.28 (0.48), residues: 128 loop : -0.41 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 407 HIS 0.010 0.001 HIS B 406 PHE 0.016 0.001 PHE B 319 TYR 0.010 0.001 TYR A 210 ARG 0.005 0.000 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9220 (t0) cc_final: 0.8872 (t0) REVERT: A 153 LEU cc_start: 0.9661 (tp) cc_final: 0.9416 (tp) REVERT: A 157 LEU cc_start: 0.9572 (mt) cc_final: 0.9305 (mt) REVERT: A 313 MET cc_start: 0.6866 (mpp) cc_final: 0.6638 (mpp) REVERT: A 377 MET cc_start: 0.8675 (tmm) cc_final: 0.8220 (tmm) REVERT: A 386 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8662 (mm-30) REVERT: A 398 MET cc_start: 0.8249 (tpt) cc_final: 0.7827 (tpt) REVERT: A 420 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: B 70 LEU cc_start: 0.8477 (mm) cc_final: 0.8267 (mm) REVERT: B 75 MET cc_start: 0.9170 (ttt) cc_final: 0.8907 (ttm) REVERT: B 79 ARG cc_start: 0.8860 (mpp80) cc_final: 0.8265 (mpp80) REVERT: B 105 LYS cc_start: 0.8956 (tptp) cc_final: 0.8513 (tppt) REVERT: B 108 TYR cc_start: 0.8076 (m-80) cc_final: 0.7694 (m-80) REVERT: B 413 MET cc_start: 0.5563 (ppp) cc_final: 0.5032 (ppp) outliers start: 13 outliers final: 10 residues processed: 138 average time/residue: 0.1473 time to fit residues: 28.9612 Evaluate side-chains 137 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 385 GLN B 433 GLN B 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7000 Z= 0.156 Angle : 0.604 8.590 9509 Z= 0.304 Chirality : 0.043 0.188 1039 Planarity : 0.004 0.037 1238 Dihedral : 8.677 136.175 984 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.49 % Allowed : 18.45 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.27 (0.29), residues: 858 helix: 0.25 (0.27), residues: 375 sheet: -0.20 (0.48), residues: 128 loop : -0.48 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 407 HIS 0.009 0.001 HIS B 406 PHE 0.018 0.001 PHE B 319 TYR 0.009 0.001 TYR B 210 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9172 (t0) cc_final: 0.8829 (t0) REVERT: A 153 LEU cc_start: 0.9647 (tp) cc_final: 0.9410 (tp) REVERT: A 157 LEU cc_start: 0.9558 (mt) cc_final: 0.9305 (mt) REVERT: A 313 MET cc_start: 0.6776 (mpp) cc_final: 0.6561 (mpp) REVERT: A 377 MET cc_start: 0.8674 (tmm) cc_final: 0.8210 (tmm) REVERT: A 386 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8634 (mm-30) REVERT: A 398 MET cc_start: 0.8212 (tpt) cc_final: 0.7862 (tpt) REVERT: A 420 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: A 430 LYS cc_start: 0.9531 (pttm) cc_final: 0.9232 (pttm) REVERT: B 21 TRP cc_start: 0.9081 (m100) cc_final: 0.8544 (m100) REVERT: B 75 MET cc_start: 0.9112 (ttt) cc_final: 0.8822 (ttm) REVERT: B 79 ARG cc_start: 0.8789 (mpp80) cc_final: 0.8177 (mpp80) REVERT: B 108 TYR cc_start: 0.8039 (m-80) cc_final: 0.7732 (m-80) REVERT: B 196 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 386 GLU cc_start: 0.8641 (pt0) cc_final: 0.8349 (pp20) REVERT: B 413 MET cc_start: 0.5570 (ppp) cc_final: 0.5140 (ppp) outliers start: 11 outliers final: 5 residues processed: 152 average time/residue: 0.1869 time to fit residues: 39.6246 Evaluate side-chains 135 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 385 GLN B 433 GLN B 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7000 Z= 0.247 Angle : 0.658 8.994 9509 Z= 0.334 Chirality : 0.045 0.174 1039 Planarity : 0.004 0.038 1238 Dihedral : 8.801 139.767 984 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.90 % Allowed : 20.76 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.37 (0.29), residues: 858 helix: 0.12 (0.26), residues: 378 sheet: -0.21 (0.48), residues: 128 loop : -0.49 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 407 HIS 0.009 0.001 HIS B 406 PHE 0.019 0.001 PHE B 319 TYR 0.019 0.001 TYR A 408 ARG 0.004 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9221 (t0) cc_final: 0.8845 (t0) REVERT: A 153 LEU cc_start: 0.9660 (tp) cc_final: 0.9436 (tp) REVERT: A 157 LEU cc_start: 0.9571 (mt) cc_final: 0.9332 (mt) REVERT: A 302 MET cc_start: 0.6476 (mmp) cc_final: 0.6000 (mtm) REVERT: A 313 MET cc_start: 0.6911 (mpp) cc_final: 0.6656 (mpp) REVERT: A 377 MET cc_start: 0.8655 (tmm) cc_final: 0.8166 (tmm) REVERT: A 386 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8670 (mm-30) REVERT: A 398 MET cc_start: 0.8255 (tpt) cc_final: 0.7920 (tpt) REVERT: A 420 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: B 1 MET cc_start: 0.6395 (mpp) cc_final: 0.5977 (pmm) REVERT: B 21 TRP cc_start: 0.9260 (m100) cc_final: 0.8730 (m100) REVERT: B 75 MET cc_start: 0.9141 (ttt) cc_final: 0.8868 (ttm) REVERT: B 79 ARG cc_start: 0.8832 (mpp80) cc_final: 0.8223 (mpp80) REVERT: B 108 TYR cc_start: 0.8102 (m-80) cc_final: 0.7791 (m-80) REVERT: B 196 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8248 (mm-30) REVERT: B 373 MET cc_start: 0.7612 (mmm) cc_final: 0.7128 (tpp) REVERT: B 386 GLU cc_start: 0.8665 (pt0) cc_final: 0.8463 (pp20) REVERT: B 413 MET cc_start: 0.5546 (ppp) cc_final: 0.5272 (ppp) outliers start: 14 outliers final: 11 residues processed: 141 average time/residue: 0.1599 time to fit residues: 31.5378 Evaluate side-chains 135 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 433 GLN B 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7000 Z= 0.182 Angle : 0.648 9.689 9509 Z= 0.323 Chirality : 0.044 0.183 1039 Planarity : 0.004 0.037 1238 Dihedral : 8.747 138.758 984 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.22 % Allowed : 22.25 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.37 (0.28), residues: 858 helix: 0.11 (0.26), residues: 378 sheet: -0.11 (0.48), residues: 128 loop : -0.52 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 103 HIS 0.010 0.001 HIS B 406 PHE 0.021 0.001 PHE B 319 TYR 0.014 0.001 TYR A 408 ARG 0.003 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9188 (t0) cc_final: 0.8803 (t0) REVERT: A 153 LEU cc_start: 0.9653 (tp) cc_final: 0.9427 (tp) REVERT: A 157 LEU cc_start: 0.9567 (mt) cc_final: 0.9324 (mt) REVERT: A 302 MET cc_start: 0.6516 (mmp) cc_final: 0.6044 (mtm) REVERT: A 377 MET cc_start: 0.8658 (tmm) cc_final: 0.8192 (tmm) REVERT: A 386 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8657 (mm-30) REVERT: A 398 MET cc_start: 0.8217 (tpt) cc_final: 0.7942 (tpt) REVERT: B 1 MET cc_start: 0.6599 (mpp) cc_final: 0.6145 (pmm) REVERT: B 21 TRP cc_start: 0.9234 (m100) cc_final: 0.8702 (m100) REVERT: B 75 MET cc_start: 0.9110 (ttt) cc_final: 0.8824 (ttm) REVERT: B 79 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8182 (mpp80) REVERT: B 108 TYR cc_start: 0.8103 (m-80) cc_final: 0.7869 (m-80) REVERT: B 166 MET cc_start: 0.8831 (tpp) cc_final: 0.8277 (ttp) REVERT: B 196 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 373 MET cc_start: 0.7541 (mmm) cc_final: 0.7118 (tpp) REVERT: B 402 LYS cc_start: 0.8903 (tppt) cc_final: 0.8634 (tppt) REVERT: B 413 MET cc_start: 0.5495 (ppp) cc_final: 0.5285 (ppp) outliers start: 9 outliers final: 9 residues processed: 144 average time/residue: 0.1827 time to fit residues: 38.4941 Evaluate side-chains 139 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7000 Z= 0.334 Angle : 0.714 9.103 9509 Z= 0.369 Chirality : 0.046 0.171 1039 Planarity : 0.005 0.040 1238 Dihedral : 9.143 145.504 984 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.44 % Allowed : 21.57 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.57 (0.28), residues: 858 helix: -0.09 (0.26), residues: 380 sheet: -0.31 (0.47), residues: 128 loop : -0.54 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 103 HIS 0.009 0.002 HIS B 406 PHE 0.026 0.002 PHE B 319 TYR 0.019 0.002 TYR A 408 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9232 (t0) cc_final: 0.8849 (t0) REVERT: A 153 LEU cc_start: 0.9666 (tp) cc_final: 0.9439 (tp) REVERT: A 157 LEU cc_start: 0.9587 (mt) cc_final: 0.9346 (mt) REVERT: A 377 MET cc_start: 0.8658 (tmm) cc_final: 0.8181 (tmm) REVERT: A 386 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8747 (mm-30) REVERT: A 398 MET cc_start: 0.8312 (tpt) cc_final: 0.8014 (tpt) REVERT: A 430 LYS cc_start: 0.9536 (pttm) cc_final: 0.9295 (pttm) REVERT: A 435 VAL cc_start: 0.8738 (t) cc_final: 0.8475 (m) REVERT: B 1 MET cc_start: 0.6732 (mpp) cc_final: 0.6309 (pmm) REVERT: B 75 MET cc_start: 0.9132 (ttt) cc_final: 0.8690 (ttm) REVERT: B 79 ARG cc_start: 0.8852 (mpp80) cc_final: 0.8292 (mpt-90) REVERT: B 302 MET cc_start: 0.7669 (ppp) cc_final: 0.6929 (ppp) REVERT: B 373 MET cc_start: 0.7901 (mmm) cc_final: 0.7516 (tpp) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.1470 time to fit residues: 29.3103 Evaluate side-chains 139 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7000 Z= 0.216 Angle : 0.696 9.962 9509 Z= 0.351 Chirality : 0.046 0.177 1039 Planarity : 0.004 0.037 1238 Dihedral : 8.984 142.897 984 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.63 % Allowed : 22.80 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.57 (0.28), residues: 858 helix: -0.06 (0.26), residues: 376 sheet: -0.25 (0.46), residues: 128 loop : -0.60 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 103 HIS 0.010 0.001 HIS B 406 PHE 0.029 0.001 PHE B 272 TYR 0.014 0.001 TYR A 408 ARG 0.003 0.000 ARG B 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9176 (t0) cc_final: 0.8779 (t0) REVERT: A 153 LEU cc_start: 0.9661 (tp) cc_final: 0.9428 (tp) REVERT: A 157 LEU cc_start: 0.9575 (mt) cc_final: 0.9325 (mt) REVERT: A 377 MET cc_start: 0.8627 (tmm) cc_final: 0.8164 (tmm) REVERT: A 386 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8736 (mm-30) REVERT: A 398 MET cc_start: 0.8271 (tpt) cc_final: 0.8041 (tpt) REVERT: B 1 MET cc_start: 0.6643 (mpp) cc_final: 0.6188 (pmm) REVERT: B 75 MET cc_start: 0.9112 (ttt) cc_final: 0.8454 (ttp) REVERT: B 79 ARG cc_start: 0.8853 (mpp80) cc_final: 0.8071 (mpt-90) REVERT: B 154 ILE cc_start: 0.9217 (mt) cc_final: 0.8872 (mt) REVERT: B 166 MET cc_start: 0.8818 (tpp) cc_final: 0.8257 (ttp) REVERT: B 402 LYS cc_start: 0.8949 (tppt) cc_final: 0.8651 (tppt) outliers start: 12 outliers final: 12 residues processed: 137 average time/residue: 0.1477 time to fit residues: 29.0950 Evaluate side-chains 138 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 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 = 0.4189 r_free = 0.4189 target = 0.120371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.094084 restraints weight = 16843.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.097883 restraints weight = 10122.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.100561 restraints weight = 7126.150| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7000 Z= 0.218 Angle : 0.692 10.485 9509 Z= 0.346 Chirality : 0.045 0.170 1039 Planarity : 0.004 0.037 1238 Dihedral : 8.938 142.692 984 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.76 % Allowed : 22.93 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.55 (0.28), residues: 858 helix: -0.04 (0.26), residues: 382 sheet: -0.23 (0.46), residues: 128 loop : -0.61 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 103 HIS 0.009 0.001 HIS B 406 PHE 0.026 0.001 PHE B 272 TYR 0.013 0.001 TYR A 408 ARG 0.003 0.000 ARG A 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.36 seconds wall clock time: 31 minutes 24.97 seconds (1884.97 seconds total)