Starting phenix.real_space_refine on Sat Dec 28 00:20:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gms_34152/12_2024/8gms_34152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gms_34152/12_2024/8gms_34152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gms_34152/12_2024/8gms_34152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gms_34152/12_2024/8gms_34152.map" model { file = "/net/cci-nas-00/data/ceres_data/8gms_34152/12_2024/8gms_34152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gms_34152/12_2024/8gms_34152.cif" } resolution = 3.31 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= 0.003 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 4380 2.51 5 N 1218 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7022 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 949 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "B" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "F" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.04, per 1000 atoms: 0.86 Number of scatterers: 7022 At special positions: 0 Unit cell: (102.34, 116.62, 104.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 12 15.00 Mg 2 11.99 O 1378 8.00 N 1218 7.00 C 4380 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 37.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.528A pdb=" N ILE A 123 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.747A pdb=" N ILE B 123 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 44 through 52 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.528A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 165 through 186 removed outlier: 4.725A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 312 through 328 removed outlier: 3.794A pdb=" N ALA F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 28 through 36 removed outlier: 6.237A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 52 removed outlier: 3.506A pdb=" N GLY G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.707A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 110 through 113 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.596A pdb=" N GLY G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 151 through 157 Processing helix chain 'G' and resid 165 through 186 removed outlier: 4.684A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 219 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 312 through 328 removed outlier: 3.513A pdb=" N ALA G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84 removed outlier: 3.892A pdb=" N GLY A 96 " --> pdb=" O LEU A 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 96 through 97 current: chain 'A' and resid 130 through 134 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 130 through 134 current: chain 'A' and resid 152 through 161 removed outlier: 3.585A pdb=" N ILE A 177 " --> pdb=" O LEU A 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 177 through 180 current: chain 'B' and resid 130 through 135 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 135 current: chain 'B' and resid 152 through 161 removed outlier: 3.750A pdb=" N ILE B 177 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 26 through 28 current: chain 'G' and resid 115 through 117 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 115 through 117 current: chain 'G' and resid 188 through 197 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 207 through 209 current: chain 'G' and resid 236 through 249 Processing sheet with id=AA3, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'F' and resid 114 through 117 removed outlier: 7.130A pdb=" N CYS F 90 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER F 117 " --> pdb=" O CYS F 90 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE F 92 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE F 141 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE F 192 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL F 143 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN F 193 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE F 64 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE F 61 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU F 223 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU F 63 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE F 225 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR F 65 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ARG F 227 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU F 241 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA F 230 " --> pdb=" O GLY F 239 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY F 239 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS F 232 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL F 237 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 195 through 197 Processing sheet with id=AA6, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.691A pdb=" N TYR F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.737A pdb=" N TYR G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2372 1.36 - 1.51: 1708 1.51 - 1.65: 2981 1.65 - 1.80: 36 1.80 - 1.95: 20 Bond restraints: 7117 Sorted by residual: bond pdb=" N LEU F 326 " pdb=" CA LEU F 326 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.30e-02 5.92e+03 6.27e+00 bond pdb=" CB THR G 76 " pdb=" CG2 THR G 76 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CG1 ILE G 141 " pdb=" CD1 ILE G 141 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 bond pdb=" CB GLN F 16 " pdb=" CG GLN F 16 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" C VAL A 193 " pdb=" O VAL A 193 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.19e-02 7.06e+03 1.04e+00 ... (remaining 7112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9423 1.85 - 3.70: 180 3.70 - 5.55: 17 5.55 - 7.41: 3 7.41 - 9.26: 1 Bond angle restraints: 9624 Sorted by residual: angle pdb=" N GLY F 204 " pdb=" CA GLY F 204 " pdb=" C GLY F 204 " ideal model delta sigma weight residual 110.87 116.28 -5.41 1.54e+00 4.22e-01 1.23e+01 angle pdb=" CA GLN F 16 " pdb=" CB GLN F 16 " pdb=" CG GLN F 16 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" N GLN A 183 " pdb=" CA GLN A 183 " pdb=" C GLN A 183 " ideal model delta sigma weight residual 114.75 110.78 3.97 1.26e+00 6.30e-01 9.93e+00 angle pdb=" CB MET F 197 " pdb=" CG MET F 197 " pdb=" SD MET F 197 " ideal model delta sigma weight residual 112.70 121.96 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" N GLU G 266 " pdb=" CA GLU G 266 " pdb=" C GLU G 266 " ideal model delta sigma weight residual 114.04 110.46 3.58 1.24e+00 6.50e-01 8.34e+00 ... (remaining 9619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3806 21.98 - 43.96: 445 43.96 - 65.93: 83 65.93 - 87.91: 18 87.91 - 109.89: 3 Dihedral angle restraints: 4355 sinusoidal: 1812 harmonic: 2543 Sorted by residual: dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 -177.62 109.89 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA HIS F 163 " pdb=" C HIS F 163 " pdb=" N MET F 164 " pdb=" CA MET F 164 " ideal model delta harmonic sigma weight residual 180.00 -163.85 -16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CB GLU G 154 " pdb=" CG GLU G 154 " pdb=" CD GLU G 154 " pdb=" OE1 GLU G 154 " ideal model delta sinusoidal sigma weight residual 0.00 -88.25 88.25 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 4352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 718 0.035 - 0.070: 266 0.070 - 0.106: 88 0.106 - 0.141: 39 0.141 - 0.176: 2 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CB ILE B 149 " pdb=" CA ILE B 149 " pdb=" CG1 ILE B 149 " pdb=" CG2 ILE B 149 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ASN F 205 " pdb=" N ASN F 205 " pdb=" C ASN F 205 " pdb=" CB ASN F 205 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE F 64 " pdb=" N ILE F 64 " pdb=" C ILE F 64 " pdb=" CB ILE F 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1110 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 308 " 0.018 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP F 308 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP F 308 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP F 308 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 308 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 308 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 308 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP F 308 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 106 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 107 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 106 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 107 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " 0.016 5.00e-02 4.00e+02 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 56 2.59 - 3.17: 5592 3.17 - 3.74: 10686 3.74 - 4.32: 14997 4.32 - 4.90: 25267 Nonbonded interactions: 56598 Sorted by model distance: nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR F 73 " pdb="MG MG F 401 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR G 42 " pdb=" OD1 ASP G 48 " model vdw 2.213 3.040 nonbonded pdb=" OG SER G 44 " pdb=" OE2 GLU G 273 " model vdw 2.248 3.040 ... (remaining 56593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 84 or resid 95 through 198)) selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.540 Find NCS groups from input model: 0.230 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.048 7117 Z= 0.244 Angle : 0.617 9.258 9624 Z= 0.351 Chirality : 0.045 0.176 1113 Planarity : 0.003 0.038 1225 Dihedral : 18.790 109.890 2725 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.55 % Allowed : 19.97 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.05 (0.27), residues: 892 helix: 1.47 (0.30), residues: 302 sheet: 0.43 (0.41), residues: 156 loop : -1.34 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP F 308 HIS 0.003 0.001 HIS A 134 PHE 0.011 0.001 PHE F 260 TYR 0.009 0.001 TYR F 218 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.780 Fit side-chains REVERT: B 78 LEU cc_start: 0.3521 (tp) cc_final: 0.3320 (tp) REVERT: F 280 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6742 (mttt) REVERT: F 308 TRP cc_start: 0.7043 (t60) cc_final: 0.6621 (t60) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.2105 time to fit residues: 29.7407 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 240 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7117 Z= 0.201 Angle : 0.510 6.846 9624 Z= 0.272 Chirality : 0.044 0.164 1113 Planarity : 0.003 0.032 1225 Dihedral : 11.947 117.378 1057 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 18.87 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.08 (0.27), residues: 892 helix: 1.62 (0.30), residues: 304 sheet: 0.46 (0.41), residues: 161 loop : -1.32 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 308 HIS 0.004 0.001 HIS A 134 PHE 0.011 0.001 PHE F 21 TYR 0.014 0.001 TYR F 218 ARG 0.003 0.000 ARG G 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.806 Fit side-chains REVERT: A 92 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: A 126 MET cc_start: 0.7256 (mmm) cc_final: 0.6977 (mtp) REVERT: A 140 ARG cc_start: 0.7476 (ptt-90) cc_final: 0.6965 (ptt90) REVERT: A 157 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7316 (mtt-85) REVERT: B 115 VAL cc_start: 0.6112 (t) cc_final: 0.5707 (p) REVERT: B 196 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7314 (pt) REVERT: F 277 LEU cc_start: 0.7347 (mm) cc_final: 0.7126 (mt) outliers start: 16 outliers final: 8 residues processed: 123 average time/residue: 0.2112 time to fit residues: 34.4294 Evaluate side-chains 115 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 137 GLN B 108 ASN F 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 7117 Z= 0.645 Angle : 0.741 7.627 9624 Z= 0.384 Chirality : 0.054 0.238 1113 Planarity : 0.005 0.041 1225 Dihedral : 12.759 128.583 1053 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.96 % Allowed : 20.66 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.81 (0.26), residues: 892 helix: 0.77 (0.28), residues: 304 sheet: -0.40 (0.39), residues: 166 loop : -1.59 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 308 HIS 0.007 0.002 HIS F 97 PHE 0.017 0.003 PHE F 255 TYR 0.025 0.003 TYR F 218 ARG 0.005 0.001 ARG F 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.690 Fit side-chains REVERT: A 92 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: A 126 MET cc_start: 0.7280 (mmm) cc_final: 0.7048 (mtp) REVERT: F 18 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5042 (tt0) REVERT: F 156 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5876 (mp0) REVERT: G 271 TYR cc_start: 0.7624 (m-80) cc_final: 0.7088 (m-80) outliers start: 36 outliers final: 26 residues processed: 130 average time/residue: 0.1922 time to fit residues: 34.0319 Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 315 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 198 ASN F 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7117 Z= 0.176 Angle : 0.504 6.388 9624 Z= 0.272 Chirality : 0.044 0.153 1113 Planarity : 0.003 0.029 1225 Dihedral : 12.237 127.557 1053 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.27 % Allowed : 22.59 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.43 (0.27), residues: 892 helix: 1.34 (0.29), residues: 306 sheet: -0.29 (0.40), residues: 168 loop : -1.55 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 308 HIS 0.003 0.001 HIS A 134 PHE 0.010 0.001 PHE F 191 TYR 0.022 0.001 TYR F 218 ARG 0.002 0.000 ARG G 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: A 140 ARG cc_start: 0.7591 (ptt-90) cc_final: 0.7226 (ptt90) REVERT: F 18 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.5226 (tt0) REVERT: F 31 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: F 156 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: F 308 TRP cc_start: 0.7024 (t60) cc_final: 0.6722 (t60) REVERT: G 76 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8591 (m) REVERT: G 271 TYR cc_start: 0.7567 (m-80) cc_final: 0.7061 (m-80) REVERT: G 274 LEU cc_start: 0.8206 (tp) cc_final: 0.7964 (tp) outliers start: 31 outliers final: 20 residues processed: 124 average time/residue: 0.2003 time to fit residues: 33.6090 Evaluate side-chains 121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7117 Z= 0.352 Angle : 0.555 6.609 9624 Z= 0.291 Chirality : 0.046 0.157 1113 Planarity : 0.004 0.032 1225 Dihedral : 12.310 128.328 1053 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.10 % Allowed : 22.87 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.45 (0.27), residues: 892 helix: 1.38 (0.29), residues: 304 sheet: -0.35 (0.40), residues: 167 loop : -1.57 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 290 HIS 0.004 0.001 HIS A 134 PHE 0.012 0.002 PHE F 191 TYR 0.020 0.001 TYR F 218 ARG 0.002 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.769 Fit side-chains REVERT: A 92 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: F 18 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5275 (tt0) REVERT: F 156 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: F 308 TRP cc_start: 0.7023 (t60) cc_final: 0.6718 (t60) REVERT: F 326 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7112 (tt) REVERT: G 159 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8073 (mm) REVERT: G 271 TYR cc_start: 0.7596 (m-80) cc_final: 0.7111 (m-80) REVERT: G 274 LEU cc_start: 0.8192 (tp) cc_final: 0.7983 (tp) REVERT: G 326 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7887 (mp) outliers start: 37 outliers final: 27 residues processed: 124 average time/residue: 0.1722 time to fit residues: 29.5406 Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7117 Z= 0.257 Angle : 0.514 6.414 9624 Z= 0.272 Chirality : 0.045 0.151 1113 Planarity : 0.003 0.032 1225 Dihedral : 12.156 128.528 1053 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.51 % Allowed : 22.73 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.29 (0.27), residues: 892 helix: 1.59 (0.30), residues: 304 sheet: -0.27 (0.40), residues: 167 loop : -1.53 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 290 HIS 0.004 0.001 HIS A 134 PHE 0.010 0.001 PHE F 191 TYR 0.022 0.001 TYR F 218 ARG 0.002 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: A 118 MET cc_start: 0.6626 (mmm) cc_final: 0.6202 (mmm) REVERT: A 121 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6592 (ptpp) REVERT: B 196 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7269 (pt) REVERT: F 18 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5236 (tt0) REVERT: F 31 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: F 156 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: F 308 TRP cc_start: 0.6967 (t60) cc_final: 0.6713 (t60) REVERT: G 271 TYR cc_start: 0.7645 (m-80) cc_final: 0.7162 (m-80) REVERT: G 274 LEU cc_start: 0.8169 (tp) cc_final: 0.7963 (tp) REVERT: G 326 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7926 (mp) outliers start: 40 outliers final: 27 residues processed: 122 average time/residue: 0.1804 time to fit residues: 30.0664 Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 85 optimal weight: 0.0870 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7117 Z= 0.412 Angle : 0.589 6.927 9624 Z= 0.305 Chirality : 0.048 0.172 1113 Planarity : 0.004 0.032 1225 Dihedral : 12.344 130.179 1053 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.65 % Allowed : 22.73 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.51 (0.27), residues: 892 helix: 1.35 (0.29), residues: 304 sheet: -0.48 (0.39), residues: 169 loop : -1.59 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 290 HIS 0.006 0.001 HIS A 134 PHE 0.012 0.002 PHE G 260 TYR 0.014 0.002 TYR F 218 ARG 0.002 0.000 ARG F 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: A 121 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6634 (ptpp) REVERT: A 180 ASP cc_start: 0.8207 (t0) cc_final: 0.7986 (t70) REVERT: F 18 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5137 (tt0) REVERT: F 31 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: F 156 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: F 308 TRP cc_start: 0.6978 (t60) cc_final: 0.6699 (t60) REVERT: G 159 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8084 (mm) REVERT: G 271 TYR cc_start: 0.7679 (m-80) cc_final: 0.7203 (m-80) REVERT: G 326 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7917 (mp) outliers start: 41 outliers final: 29 residues processed: 124 average time/residue: 0.1670 time to fit residues: 28.8963 Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN F 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7117 Z= 0.174 Angle : 0.506 6.348 9624 Z= 0.266 Chirality : 0.043 0.145 1113 Planarity : 0.003 0.034 1225 Dihedral : 11.938 128.282 1053 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.41 % Allowed : 23.83 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.12 (0.28), residues: 892 helix: 1.79 (0.30), residues: 304 sheet: -0.14 (0.42), residues: 158 loop : -1.48 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 290 HIS 0.003 0.001 HIS A 134 PHE 0.008 0.001 PHE F 191 TYR 0.007 0.001 TYR F 218 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 118 MET cc_start: 0.6806 (mmm) cc_final: 0.6373 (mmm) REVERT: A 121 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6323 (ptpp) REVERT: F 18 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5194 (tt0) REVERT: F 31 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: F 156 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6005 (mp0) REVERT: F 178 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8572 (mt) REVERT: F 308 TRP cc_start: 0.6890 (t60) cc_final: 0.6632 (t60) REVERT: G 271 TYR cc_start: 0.7640 (m-80) cc_final: 0.7204 (m-80) REVERT: G 274 LEU cc_start: 0.8195 (tp) cc_final: 0.7932 (tp) REVERT: G 326 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7853 (mp) outliers start: 32 outliers final: 20 residues processed: 126 average time/residue: 0.2065 time to fit residues: 35.0768 Evaluate side-chains 124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7117 Z= 0.374 Angle : 0.590 7.940 9624 Z= 0.304 Chirality : 0.048 0.202 1113 Planarity : 0.004 0.033 1225 Dihedral : 12.276 130.554 1053 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.82 % Allowed : 23.42 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.41 (0.27), residues: 892 helix: 1.49 (0.30), residues: 306 sheet: -0.39 (0.41), residues: 163 loop : -1.59 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 290 HIS 0.005 0.001 HIS A 134 PHE 0.012 0.002 PHE G 260 TYR 0.009 0.001 TYR F 65 ARG 0.002 0.000 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.857 Fit side-chains REVERT: A 92 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: F 18 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5181 (tt0) REVERT: F 31 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: F 156 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: F 308 TRP cc_start: 0.6992 (t60) cc_final: 0.6687 (t60) REVERT: G 271 TYR cc_start: 0.7685 (m-80) cc_final: 0.7227 (m-80) REVERT: G 274 LEU cc_start: 0.8251 (tp) cc_final: 0.7974 (tp) REVERT: G 326 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7924 (mp) outliers start: 35 outliers final: 26 residues processed: 120 average time/residue: 0.1690 time to fit residues: 28.7076 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7117 Z= 0.181 Angle : 0.524 7.787 9624 Z= 0.272 Chirality : 0.044 0.174 1113 Planarity : 0.003 0.035 1225 Dihedral : 12.052 129.390 1053 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.58 % Allowed : 24.52 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.12 (0.27), residues: 892 helix: 1.79 (0.30), residues: 304 sheet: -0.09 (0.43), residues: 153 loop : -1.49 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 290 HIS 0.006 0.001 HIS A 134 PHE 0.010 0.001 PHE F 191 TYR 0.023 0.001 TYR F 218 ARG 0.002 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.758 Fit side-chains REVERT: A 92 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: A 120 MET cc_start: 0.6875 (mmm) cc_final: 0.6625 (mmm) REVERT: A 157 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.7086 (mtt-85) REVERT: F 18 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.5152 (tt0) REVERT: F 31 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: F 156 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: F 308 TRP cc_start: 0.6865 (t60) cc_final: 0.6659 (t60) REVERT: G 271 TYR cc_start: 0.7665 (m-80) cc_final: 0.7197 (m-80) REVERT: G 274 LEU cc_start: 0.8233 (tp) cc_final: 0.7943 (tp) REVERT: G 326 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7846 (mp) outliers start: 26 outliers final: 21 residues processed: 112 average time/residue: 0.1818 time to fit residues: 28.0512 Evaluate side-chains 126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 171 ASN ** 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 = 0.4060 r_free = 0.4060 target = 0.186841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139811 restraints weight = 7910.242| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.87 r_work: 0.3231 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7117 Z= 0.281 Angle : 0.551 7.922 9624 Z= 0.283 Chirality : 0.046 0.171 1113 Planarity : 0.003 0.034 1225 Dihedral : 12.124 129.478 1053 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.55 % Allowed : 23.42 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.17 (0.27), residues: 892 helix: 1.73 (0.30), residues: 304 sheet: -0.22 (0.42), residues: 155 loop : -1.47 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 290 HIS 0.003 0.001 HIS A 134 PHE 0.010 0.001 PHE F 191 TYR 0.015 0.001 TYR F 218 ARG 0.002 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.19 seconds wall clock time: 31 minutes 56.55 seconds (1916.55 seconds total)