Starting phenix.real_space_refine on Fri Jul 19 01:22:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbb_37419/07_2024/8wbb_37419_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbb_37419/07_2024/8wbb_37419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbb_37419/07_2024/8wbb_37419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbb_37419/07_2024/8wbb_37419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbb_37419/07_2024/8wbb_37419_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbb_37419/07_2024/8wbb_37419_neut.cif" } resolution = 2.9 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= 0.167 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 42 5.16 5 C 3440 2.51 5 N 937 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a GLU 146": "OE1" <-> "OE2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "a GLU 289": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5449 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2736 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Chain breaks: 1 Chain: "a" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2713 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Time building chain proxies: 4.57, per 1000 atoms: 0.84 Number of scatterers: 5449 At special positions: 0 Unit cell: (87.55, 68.85, 113.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1030 8.00 N 937 7.00 C 3440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.04 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 19.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 40 through 53 removed outlier: 3.634A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.526A pdb=" N MET A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.533A pdb=" N LEU A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.561A pdb=" N ARG A 148 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 removed outlier: 4.021A pdb=" N LEU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.500A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.694A pdb=" N MET A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.524A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'a' and resid 40 through 53 removed outlier: 3.706A pdb=" N GLU a 51 " --> pdb=" O LEU a 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP a 52 " --> pdb=" O ASN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 71 removed outlier: 3.539A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 82 removed outlier: 3.551A pdb=" N GLY a 82 " --> pdb=" O VAL a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.842A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.729A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.527A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.668A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 271' Processing helix chain 'a' and resid 341 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.326A pdb=" N LYS A 14 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA A 5 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 16 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS a 14 " --> pdb=" O ALA a 5 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 19 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.543A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.735A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.750A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE A 212 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.071A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 32 through 35 removed outlier: 6.250A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 56 through 57 removed outlier: 6.636A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.812A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.020A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 342 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: 1.61 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 911 1.31 - 1.44: 1564 1.44 - 1.57: 3057 1.57 - 1.70: 0 1.70 - 1.83: 60 Bond restraints: 5592 Sorted by residual: bond pdb=" C LEU a 42 " pdb=" O LEU a 42 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.19e-02 7.06e+03 2.39e+01 bond pdb=" CA LEU a 42 " pdb=" C LEU a 42 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.29e-02 6.01e+03 1.66e+01 bond pdb=" CA ARG a 41 " pdb=" C ARG a 41 " ideal model delta sigma weight residual 1.522 1.466 0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N ARG a 41 " pdb=" CA ARG a 41 " ideal model delta sigma weight residual 1.457 1.409 0.048 1.29e-02 6.01e+03 1.38e+01 bond pdb=" CA ALA a 40 " pdb=" CB ALA a 40 " ideal model delta sigma weight residual 1.537 1.491 0.046 1.38e-02 5.25e+03 1.13e+01 ... (remaining 5587 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 156 106.58 - 113.44: 3058 113.44 - 120.29: 1864 120.29 - 127.15: 2413 127.15 - 134.00: 97 Bond angle restraints: 7588 Sorted by residual: angle pdb=" N ARG a 41 " pdb=" CA ARG a 41 " pdb=" C ARG a 41 " ideal model delta sigma weight residual 112.90 105.24 7.66 1.31e+00 5.83e-01 3.41e+01 angle pdb=" CA MET a 162 " pdb=" CB MET a 162 " pdb=" CG MET a 162 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA LYS a 11 " pdb=" CB LYS a 11 " pdb=" CG LYS a 11 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N ALA a 40 " pdb=" CA ALA a 40 " pdb=" CB ALA a 40 " ideal model delta sigma weight residual 110.90 106.46 4.44 1.33e+00 5.65e-01 1.11e+01 angle pdb=" C LYS a 11 " pdb=" N GLU a 12 " pdb=" CA GLU a 12 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 ... (remaining 7583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2742 17.96 - 35.93: 408 35.93 - 53.89: 126 53.89 - 71.85: 25 71.85 - 89.82: 12 Dihedral angle restraints: 3313 sinusoidal: 1344 harmonic: 1969 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 169.63 -76.63 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -154.99 68.99 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS A 15 " pdb=" CB CYS A 15 " ideal model delta sinusoidal sigma weight residual 93.00 54.68 38.32 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 445 0.029 - 0.058: 247 0.058 - 0.087: 60 0.087 - 0.115: 47 0.115 - 0.144: 9 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA ILE a 22 " pdb=" N ILE a 22 " pdb=" C ILE a 22 " pdb=" CB ILE a 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 22 " pdb=" N ILE A 22 " pdb=" C ILE A 22 " pdb=" CB ILE A 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE a 243 " pdb=" N ILE a 243 " pdb=" C ILE a 243 " pdb=" CB ILE a 243 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 805 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 35 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO a 36 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO a 36 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO a 36 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET a 162 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C MET a 162 " -0.031 2.00e-02 2.50e+03 pdb=" O MET a 162 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE a 163 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS a 280 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO a 281 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO a 281 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 281 " -0.021 5.00e-02 4.00e+02 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 599 2.75 - 3.29: 4700 3.29 - 3.83: 8466 3.83 - 4.36: 10523 4.36 - 4.90: 18925 Nonbonded interactions: 43213 Sorted by model distance: nonbonded pdb=" OG SER A 59 " pdb=" OD2 ASP A 136 " model vdw 2.213 2.440 nonbonded pdb=" OG SER a 38 " pdb=" O LYS a 116 " model vdw 2.230 2.440 nonbonded pdb=" NZ LYS a 33 " pdb=" OE1 GLN a 35 " model vdw 2.267 2.520 nonbonded pdb=" O ASP A 23 " pdb=" OG1 THR A 27 " model vdw 2.277 2.440 nonbonded pdb=" NH1 ARG A 172 " pdb=" OG SER A 176 " model vdw 2.312 2.520 ... (remaining 43208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 118 or resid 128 through 352)) selection = chain 'a' } 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: 1.130 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.170 Find NCS groups from input model: 0.240 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.004 0.058 5592 Z= 0.228 Angle : 0.620 7.655 7588 Z= 0.327 Chirality : 0.043 0.144 808 Planarity : 0.004 0.049 967 Dihedral : 19.177 89.816 2020 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.58 % Favored : 94.27 % Rotamer: Outliers : 0.51 % Allowed : 30.69 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.79 (0.30), residues: 681 helix: -0.39 (0.66), residues: 71 sheet: -1.27 (0.47), residues: 121 loop : -1.35 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 PHE 0.013 0.002 PHE A 20 TYR 0.010 0.001 TYR a 256 ARG 0.006 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.639 Fit side-chains REVERT: a 147 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7461 (mtm-85) REVERT: a 306 LYS cc_start: 0.8096 (pttt) cc_final: 0.7860 (pttp) outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 1.1367 time to fit residues: 100.4258 Evaluate side-chains 72 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 62 ARG Chi-restraints excluded: chain a residue 322 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 84 HIS A 208 GLN A 293 HIS a 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5592 Z= 0.214 Angle : 0.573 5.916 7588 Z= 0.293 Chirality : 0.043 0.157 808 Planarity : 0.004 0.036 967 Dihedral : 5.184 47.294 741 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.61 % Favored : 93.25 % Rotamer: Outliers : 6.41 % Allowed : 26.98 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.59 (0.31), residues: 681 helix: 0.39 (0.67), residues: 71 sheet: -1.17 (0.45), residues: 138 loop : -1.30 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 PHE 0.012 0.002 PHE a 20 TYR 0.011 0.001 TYR a 256 ARG 0.005 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 72 time to evaluate : 0.626 Fit side-chains REVERT: a 62 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6150 (mpt180) REVERT: a 147 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7520 (mtm-85) REVERT: a 192 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8102 (mtpp) REVERT: a 306 LYS cc_start: 0.8157 (pttt) cc_final: 0.7853 (pttp) REVERT: a 310 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7338 (mp10) outliers start: 38 outliers final: 14 residues processed: 99 average time/residue: 0.9760 time to fit residues: 101.9269 Evaluate side-chains 84 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 62 ARG Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 0.0170 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5592 Z= 0.277 Angle : 0.590 6.285 7588 Z= 0.301 Chirality : 0.045 0.169 808 Planarity : 0.004 0.035 967 Dihedral : 5.138 47.408 737 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 6.91 % Allowed : 27.15 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.51 (0.30), residues: 681 helix: 0.76 (0.67), residues: 71 sheet: -1.18 (0.44), residues: 136 loop : -1.28 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.005 0.001 HIS a 254 PHE 0.020 0.002 PHE a 20 TYR 0.012 0.001 TYR a 256 ARG 0.004 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 70 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 172 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8145 (mtt180) REVERT: A 214 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7977 (tttt) REVERT: a 75 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7870 (mp) REVERT: a 147 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7625 (mtm-85) REVERT: a 172 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8385 (mtt-85) REVERT: a 192 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8128 (mtpp) REVERT: a 292 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7974 (p0) REVERT: a 306 LYS cc_start: 0.8097 (pttt) cc_final: 0.7784 (pttp) REVERT: a 310 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7351 (mp10) outliers start: 41 outliers final: 20 residues processed: 100 average time/residue: 0.9134 time to fit residues: 96.5947 Evaluate side-chains 94 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5592 Z= 0.233 Angle : 0.565 5.859 7588 Z= 0.289 Chirality : 0.044 0.173 808 Planarity : 0.004 0.035 967 Dihedral : 4.607 35.346 733 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.41 % Allowed : 27.99 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.40 (0.30), residues: 681 helix: 0.87 (0.66), residues: 73 sheet: -1.08 (0.45), residues: 131 loop : -1.23 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 PHE 0.013 0.002 PHE a 20 TYR 0.011 0.001 TYR a 256 ARG 0.003 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 66 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 172 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8186 (mtt180) REVERT: A 214 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (tttt) REVERT: a 147 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7628 (mtm-85) REVERT: a 172 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8450 (mtt-85) REVERT: a 192 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8136 (mtpp) REVERT: a 292 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7971 (p0) REVERT: a 306 LYS cc_start: 0.8018 (pttt) cc_final: 0.7805 (ptmt) REVERT: a 310 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7374 (mp10) outliers start: 38 outliers final: 21 residues processed: 94 average time/residue: 0.9583 time to fit residues: 95.0485 Evaluate side-chains 92 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5592 Z= 0.162 Angle : 0.522 5.785 7588 Z= 0.268 Chirality : 0.042 0.163 808 Planarity : 0.003 0.034 967 Dihedral : 4.399 35.855 733 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 28.33 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.29 (0.31), residues: 681 helix: 1.09 (0.67), residues: 73 sheet: -1.06 (0.45), residues: 131 loop : -1.16 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.002 0.001 HIS A 254 PHE 0.008 0.001 PHE A 323 TYR 0.009 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 66 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8175 (tttt) cc_final: 0.7541 (mptm) REVERT: A 172 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8139 (mtt180) REVERT: a 51 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: a 147 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7615 (mtm-85) REVERT: a 172 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8548 (mtt-85) REVERT: a 192 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8081 (mtpp) REVERT: a 292 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7898 (p0) REVERT: a 306 LYS cc_start: 0.8022 (pttt) cc_final: 0.7819 (ptmt) REVERT: a 310 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7319 (mp10) outliers start: 33 outliers final: 16 residues processed: 93 average time/residue: 1.0151 time to fit residues: 99.5930 Evaluate side-chains 88 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 5592 Z= 0.467 Angle : 0.683 7.623 7588 Z= 0.347 Chirality : 0.049 0.174 808 Planarity : 0.004 0.037 967 Dihedral : 5.069 34.503 733 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.91 % Allowed : 27.49 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.56 (0.30), residues: 681 helix: 0.68 (0.66), residues: 75 sheet: -1.25 (0.43), residues: 144 loop : -1.31 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 210 HIS 0.007 0.001 HIS a 254 PHE 0.016 0.002 PHE A 323 TYR 0.014 0.002 TYR a 256 ARG 0.003 0.000 ARG a 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 0.681 Fit side-chains REVERT: A 85 ASP cc_start: 0.7442 (t0) cc_final: 0.7161 (p0) REVERT: A 172 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8305 (mtt-85) REVERT: A 214 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8008 (tttt) REVERT: a 147 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7672 (mtm-85) REVERT: a 172 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8465 (mtt-85) REVERT: a 192 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8131 (mtpp) REVERT: a 292 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8102 (p0) REVERT: a 306 LYS cc_start: 0.7980 (pttt) cc_final: 0.7759 (ptmt) REVERT: a 310 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7378 (mp10) outliers start: 41 outliers final: 22 residues processed: 97 average time/residue: 0.9118 time to fit residues: 93.6977 Evaluate side-chains 90 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 172 ARG Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5592 Z= 0.163 Angle : 0.533 6.038 7588 Z= 0.273 Chirality : 0.042 0.178 808 Planarity : 0.003 0.035 967 Dihedral : 4.535 36.024 733 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.22 % Allowed : 30.02 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.38 (0.30), residues: 681 helix: 1.11 (0.67), residues: 73 sheet: -1.14 (0.45), residues: 131 loop : -1.23 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.002 0.001 HIS A 254 PHE 0.011 0.001 PHE A 323 TYR 0.010 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.619 Fit side-chains REVERT: A 94 LYS cc_start: 0.8219 (tttt) cc_final: 0.7536 (mptm) REVERT: A 172 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8198 (mtt180) REVERT: A 245 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8593 (tttp) REVERT: a 87 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8357 (p) REVERT: a 147 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7581 (mtm-85) REVERT: a 192 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: a 306 LYS cc_start: 0.8001 (pttt) cc_final: 0.7782 (ptmt) REVERT: a 310 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7287 (mp10) outliers start: 25 outliers final: 14 residues processed: 87 average time/residue: 0.9966 time to fit residues: 91.5202 Evaluate side-chains 84 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5592 Z= 0.249 Angle : 0.571 6.334 7588 Z= 0.290 Chirality : 0.044 0.178 808 Planarity : 0.003 0.035 967 Dihedral : 4.657 35.613 733 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.23 % Allowed : 29.17 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.42 (0.31), residues: 681 helix: 1.18 (0.66), residues: 73 sheet: -1.48 (0.41), residues: 152 loop : -1.13 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 PHE 0.011 0.002 PHE A 323 TYR 0.011 0.001 TYR a 256 ARG 0.002 0.000 ARG a 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 65 time to evaluate : 0.648 Fit side-chains REVERT: A 85 ASP cc_start: 0.7483 (t0) cc_final: 0.7209 (p0) REVERT: A 94 LYS cc_start: 0.8255 (tttt) cc_final: 0.7542 (mptm) REVERT: A 172 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8205 (mtt180) REVERT: A 245 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8620 (tttp) REVERT: a 87 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8341 (p) REVERT: a 147 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7629 (mtm-85) REVERT: a 192 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: a 292 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7996 (p0) REVERT: a 306 LYS cc_start: 0.7984 (pttt) cc_final: 0.7764 (ptmt) REVERT: a 310 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7355 (mp10) outliers start: 31 outliers final: 20 residues processed: 91 average time/residue: 0.9507 time to fit residues: 91.5753 Evaluate side-chains 90 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5592 Z= 0.142 Angle : 0.524 8.252 7588 Z= 0.264 Chirality : 0.042 0.173 808 Planarity : 0.003 0.036 967 Dihedral : 4.306 35.996 733 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.71 % Allowed : 30.35 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.24 (0.31), residues: 681 helix: 1.38 (0.65), residues: 73 sheet: -1.12 (0.44), residues: 131 loop : -1.14 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.002 0.001 HIS A 254 PHE 0.008 0.001 PHE A 277 TYR 0.008 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.637 Fit side-chains REVERT: A 94 LYS cc_start: 0.8221 (tttt) cc_final: 0.7546 (mptm) REVERT: A 172 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8191 (mtt180) REVERT: a 87 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8384 (p) REVERT: a 147 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7580 (mtm-85) REVERT: a 306 LYS cc_start: 0.8018 (pttt) cc_final: 0.7802 (ptmt) outliers start: 22 outliers final: 15 residues processed: 83 average time/residue: 0.9507 time to fit residues: 83.5496 Evaluate side-chains 79 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS a 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5592 Z= 0.159 Angle : 0.531 8.177 7588 Z= 0.266 Chirality : 0.042 0.169 808 Planarity : 0.003 0.035 967 Dihedral : 4.307 35.748 733 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.20 % Allowed : 31.03 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.18 (0.31), residues: 681 helix: 1.57 (0.65), residues: 73 sheet: -1.09 (0.45), residues: 131 loop : -1.12 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 PHE 0.009 0.001 PHE a 277 TYR 0.009 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.653 Fit side-chains REVERT: A 94 LYS cc_start: 0.8243 (tttt) cc_final: 0.7550 (mptm) REVERT: A 172 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8172 (mtt180) REVERT: a 87 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8379 (p) REVERT: a 147 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7597 (mtm-85) REVERT: a 292 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7890 (p0) REVERT: a 306 LYS cc_start: 0.8010 (pttt) cc_final: 0.7797 (ptmt) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 0.9300 time to fit residues: 81.8840 Evaluate side-chains 83 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 92 ASP Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 292 ASP Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS a 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131914 restraints weight = 5285.688| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.07 r_work: 0.3316 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5592 Z= 0.127 Angle : 0.507 8.252 7588 Z= 0.254 Chirality : 0.041 0.167 808 Planarity : 0.003 0.035 967 Dihedral : 4.112 35.614 733 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.87 % Allowed : 31.20 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.31), residues: 681 helix: 1.74 (0.64), residues: 73 sheet: -1.05 (0.45), residues: 131 loop : -1.06 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.002 0.001 HIS A 254 PHE 0.008 0.001 PHE A 20 TYR 0.007 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.42 seconds wall clock time: 42 minutes 34.37 seconds (2554.37 seconds total)