Starting phenix.real_space_refine on Fri Feb 14 07:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7agf_11778/02_2025/7agf_11778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7agf_11778/02_2025/7agf_11778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7agf_11778/02_2025/7agf_11778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7agf_11778/02_2025/7agf_11778.map" model { file = "/net/cci-nas-00/data/ceres_data/7agf_11778/02_2025/7agf_11778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7agf_11778/02_2025/7agf_11778.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 36 5.16 5 C 6354 2.51 5 N 1641 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10071 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "E" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Restraints were copied for chains: C, B, D, F Time building chain proxies: 5.09, per 1000 atoms: 0.51 Number of scatterers: 10071 At special positions: 0 Unit cell: (126.75, 131.3, 98.8, 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 36 16.00 O 2040 8.00 N 1641 7.00 C 6354 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: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 7.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU A 250 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.576A pdb=" N MET D 296 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.577A pdb=" N MET E 296 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 removed outlier: 3.578A pdb=" N MET F 296 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU B 250 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199 removed outlier: 5.609A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.316A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU D 128 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 173 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 242 through 245 removed outlier: 4.165A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.735A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.315A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU E 128 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 173 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 242 through 245 removed outlier: 4.164A pdb=" N THR E 242 " --> pdb=" O VAL E 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 259 through 265 removed outlier: 6.734A pdb=" N SER E 302 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 120 removed outlier: 6.315A pdb=" N PHE F 115 " --> pdb=" O GLN F 210 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG F 212 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY F 117 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU F 214 " --> pdb=" O GLY F 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 119 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR F 187 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU F 154 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR F 189 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU F 128 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR F 173 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 242 through 245 removed outlier: 4.165A pdb=" N THR F 242 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 265 removed outlier: 6.735A pdb=" N SER F 302 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.608A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AC4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AC5, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.608A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 219 through 220 258 hydrogen bonds defined for protein. 630 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: 2.52 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3318 1.34 - 1.46: 2243 1.46 - 1.58: 4648 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 10269 Sorted by residual: bond pdb=" CD ARG E 180 " pdb=" NE ARG E 180 " ideal model delta sigma weight residual 1.458 1.433 0.025 1.40e-02 5.10e+03 3.21e+00 bond pdb=" CD ARG D 180 " pdb=" NE ARG D 180 " ideal model delta sigma weight residual 1.458 1.433 0.025 1.40e-02 5.10e+03 3.19e+00 bond pdb=" CD ARG F 180 " pdb=" NE ARG F 180 " ideal model delta sigma weight residual 1.458 1.434 0.024 1.40e-02 5.10e+03 2.99e+00 bond pdb=" CZ ARG D 180 " pdb=" NH2 ARG D 180 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" CZ ARG E 180 " pdb=" NH2 ARG E 180 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.77e+00 ... (remaining 10264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13622 2.26 - 4.51: 316 4.51 - 6.77: 57 6.77 - 9.03: 9 9.03 - 11.28: 6 Bond angle restraints: 14010 Sorted by residual: angle pdb=" C ARG D 316 " pdb=" N SER D 317 " pdb=" CA SER D 317 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ARG F 316 " pdb=" N SER F 317 " pdb=" CA SER F 317 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ARG E 316 " pdb=" N SER E 317 " pdb=" CA SER E 317 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C ILE E 284 " pdb=" N VAL E 285 " pdb=" CA VAL E 285 " ideal model delta sigma weight residual 122.91 117.62 5.29 1.43e+00 4.89e-01 1.37e+01 angle pdb=" C ILE D 284 " pdb=" N VAL D 285 " pdb=" CA VAL D 285 " ideal model delta sigma weight residual 122.91 117.63 5.28 1.43e+00 4.89e-01 1.36e+01 ... (remaining 14005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 5603 15.86 - 31.72: 414 31.72 - 47.58: 87 47.58 - 63.44: 25 63.44 - 79.30: 15 Dihedral angle restraints: 6144 sinusoidal: 2352 harmonic: 3792 Sorted by residual: dihedral pdb=" CA SER E 153 " pdb=" C SER E 153 " pdb=" N LEU E 154 " pdb=" CA LEU E 154 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER F 153 " pdb=" C SER F 153 " pdb=" N LEU F 154 " pdb=" CA LEU F 154 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER D 153 " pdb=" C SER D 153 " pdb=" N LEU D 154 " pdb=" CA LEU D 154 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 922 0.040 - 0.081: 514 0.081 - 0.121: 163 0.121 - 0.161: 44 0.161 - 0.201: 10 Chirality restraints: 1653 Sorted by residual: chirality pdb=" CA GLU E 155 " pdb=" N GLU E 155 " pdb=" C GLU E 155 " pdb=" CB GLU E 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU F 155 " pdb=" N GLU F 155 " pdb=" C GLU F 155 " pdb=" CB GLU F 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU D 155 " pdb=" N GLU D 155 " pdb=" C GLU D 155 " pdb=" CB GLU D 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1650 not shown) Planarity restraints: 1815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " -0.043 2.00e-02 2.50e+03 4.82e-02 5.81e+01 pdb=" CG TRP A 135 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 135 " -0.043 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP C 135 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP C 135 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 135 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 135 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 135 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP C 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 135 " 0.042 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP B 135 " -0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP B 135 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 135 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 135 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 135 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 135 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP B 135 " 0.003 2.00e-02 2.50e+03 ... (remaining 1812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 295 2.69 - 3.24: 9486 3.24 - 3.79: 16487 3.79 - 4.35: 22330 4.35 - 4.90: 36442 Nonbonded interactions: 85040 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR C 319 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR B 319 " pdb=" OH TYR C 319 " model vdw 2.145 3.040 nonbonded pdb=" OE1 GLU D 170 " pdb=" OH TYR D 172 " model vdw 2.244 3.040 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.244 3.040 ... (remaining 85035 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 2.170 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10269 Z= 0.417 Angle : 0.878 11.283 14010 Z= 0.489 Chirality : 0.054 0.201 1653 Planarity : 0.005 0.048 1815 Dihedral : 13.216 79.297 3684 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1275 helix: -3.96 (0.41), residues: 36 sheet: -0.79 (0.24), residues: 453 loop : -0.36 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.011 TRP A 135 HIS 0.004 0.001 HIS C 266 PHE 0.019 0.003 PHE D 301 TYR 0.023 0.002 TYR C 174 ARG 0.010 0.002 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 300 ASP cc_start: 0.6668 (t0) cc_final: 0.6404 (t0) REVERT: C 276 MET cc_start: 0.6375 (mtp) cc_final: 0.6085 (mtm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2710 time to fit residues: 90.8034 Evaluate side-chains 183 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN D 165 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN E 165 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN F 165 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.069594 restraints weight = 19857.707| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.44 r_work: 0.2804 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10269 Z= 0.190 Angle : 0.603 8.590 14010 Z= 0.316 Chirality : 0.046 0.148 1653 Planarity : 0.004 0.035 1815 Dihedral : 5.439 21.722 1365 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.87 % Allowed : 8.29 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1275 helix: -3.81 (0.50), residues: 36 sheet: -0.91 (0.23), residues: 468 loop : -0.15 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP C 135 HIS 0.001 0.000 HIS A 266 PHE 0.018 0.002 PHE D 301 TYR 0.025 0.001 TYR D 319 ARG 0.004 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7285 (mm-40) REVERT: D 210 GLN cc_start: 0.8814 (mp10) cc_final: 0.8413 (mp10) REVERT: D 271 TYR cc_start: 0.6560 (m-80) cc_final: 0.6148 (m-80) REVERT: B 276 MET cc_start: 0.8664 (mtm) cc_final: 0.8047 (mtm) REVERT: B 303 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8789 (mm-30) REVERT: B 323 GLU cc_start: 0.8668 (tp30) cc_final: 0.8054 (tp30) REVERT: C 250 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: C 276 MET cc_start: 0.8738 (mtp) cc_final: 0.8419 (mtm) REVERT: C 279 GLN cc_start: 0.8020 (mt0) cc_final: 0.7563 (mt0) REVERT: C 323 GLU cc_start: 0.8663 (tp30) cc_final: 0.8111 (tp30) outliers start: 10 outliers final: 7 residues processed: 184 average time/residue: 0.2568 time to fit residues: 63.8070 Evaluate side-chains 178 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069967 restraints weight = 20127.611| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.47 r_work: 0.2821 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10269 Z= 0.160 Angle : 0.545 7.905 14010 Z= 0.288 Chirality : 0.045 0.146 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.925 18.346 1365 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.05 % Allowed : 8.99 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1275 helix: -3.50 (0.58), residues: 36 sheet: -0.77 (0.23), residues: 468 loop : 0.01 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 135 HIS 0.001 0.000 HIS A 266 PHE 0.020 0.002 PHE D 301 TYR 0.012 0.001 TYR E 149 ARG 0.005 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 GLN cc_start: 0.7570 (mm110) cc_final: 0.7364 (mm-40) REVERT: A 319 TYR cc_start: 0.8904 (m-80) cc_final: 0.8547 (m-80) REVERT: D 210 GLN cc_start: 0.8880 (mp10) cc_final: 0.8525 (mp10) REVERT: D 226 LYS cc_start: 0.5719 (ttpt) cc_final: 0.5357 (tttp) REVERT: D 271 TYR cc_start: 0.6520 (m-80) cc_final: 0.6230 (m-80) REVERT: E 193 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7468 (tpp80) REVERT: B 250 GLU cc_start: 0.8858 (pt0) cc_final: 0.8625 (pt0) REVERT: B 323 GLU cc_start: 0.8666 (tp30) cc_final: 0.8099 (tp30) REVERT: C 181 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8933 (t0) REVERT: C 236 MET cc_start: 0.9403 (mmp) cc_final: 0.9127 (mmt) REVERT: C 250 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: C 276 MET cc_start: 0.8804 (mtp) cc_final: 0.8467 (mtp) REVERT: C 319 TYR cc_start: 0.8952 (m-80) cc_final: 0.8712 (m-80) REVERT: C 323 GLU cc_start: 0.8666 (tp30) cc_final: 0.8099 (tp30) outliers start: 12 outliers final: 6 residues processed: 191 average time/residue: 0.2790 time to fit residues: 72.5169 Evaluate side-chains 182 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN C 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065988 restraints weight = 19962.974| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.42 r_work: 0.2743 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10269 Z= 0.303 Angle : 0.588 8.351 14010 Z= 0.308 Chirality : 0.046 0.145 1653 Planarity : 0.003 0.035 1815 Dihedral : 5.088 18.205 1365 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.83 % Allowed : 10.21 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1275 helix: -3.22 (0.62), residues: 36 sheet: -0.69 (0.24), residues: 468 loop : 0.08 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 135 HIS 0.002 0.001 HIS A 266 PHE 0.020 0.002 PHE F 301 TYR 0.014 0.002 TYR E 149 ARG 0.005 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8841 (pt0) cc_final: 0.8529 (pt0) REVERT: A 279 GLN cc_start: 0.7716 (mm110) cc_final: 0.7498 (mm-40) REVERT: A 291 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8004 (ttm-80) REVERT: A 319 TYR cc_start: 0.8888 (m-80) cc_final: 0.8330 (m-80) REVERT: D 112 GLN cc_start: 0.8476 (pm20) cc_final: 0.8253 (pm20) REVERT: D 210 GLN cc_start: 0.8833 (mp10) cc_final: 0.8441 (mp10) REVERT: D 271 TYR cc_start: 0.6734 (m-80) cc_final: 0.6375 (m-80) REVERT: D 319 TYR cc_start: 0.9376 (t80) cc_final: 0.9150 (t80) REVERT: F 112 GLN cc_start: 0.8432 (pm20) cc_final: 0.8216 (pm20) REVERT: F 210 GLN cc_start: 0.8488 (mp10) cc_final: 0.7961 (mp10) REVERT: B 181 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8924 (t0) REVERT: B 250 GLU cc_start: 0.8891 (pt0) cc_final: 0.8658 (pt0) REVERT: B 279 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: B 323 GLU cc_start: 0.8766 (tp30) cc_final: 0.8102 (tp30) REVERT: C 196 GLU cc_start: 0.8270 (tp30) cc_final: 0.7836 (tp30) REVERT: C 250 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: C 291 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: C 319 TYR cc_start: 0.8792 (m-80) cc_final: 0.8568 (m-80) REVERT: C 323 GLU cc_start: 0.8753 (tp30) cc_final: 0.8140 (tp30) outliers start: 21 outliers final: 7 residues processed: 191 average time/residue: 0.2886 time to fit residues: 73.7695 Evaluate side-chains 188 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066913 restraints weight = 20000.191| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.41 r_work: 0.2759 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10269 Z= 0.244 Angle : 0.561 8.304 14010 Z= 0.296 Chirality : 0.046 0.149 1653 Planarity : 0.003 0.025 1815 Dihedral : 4.954 17.546 1365 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.92 % Allowed : 10.03 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1275 helix: -2.89 (0.69), residues: 36 sheet: -0.56 (0.24), residues: 462 loop : 0.02 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 296 HIS 0.001 0.000 HIS A 266 PHE 0.021 0.002 PHE F 301 TYR 0.015 0.002 TYR E 149 ARG 0.006 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8829 (pt0) cc_final: 0.8479 (pt0) REVERT: A 291 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.7965 (ttm-80) REVERT: A 323 GLU cc_start: 0.8901 (tp30) cc_final: 0.8692 (mm-30) REVERT: D 112 GLN cc_start: 0.8489 (pm20) cc_final: 0.8245 (pm20) REVERT: D 210 GLN cc_start: 0.8830 (mp10) cc_final: 0.8437 (mp10) REVERT: D 271 TYR cc_start: 0.6777 (m-80) cc_final: 0.6431 (m-80) REVERT: F 112 GLN cc_start: 0.8445 (pm20) cc_final: 0.8205 (pm20) REVERT: F 210 GLN cc_start: 0.8512 (mp10) cc_final: 0.7966 (mp10) REVERT: B 181 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8922 (t0) REVERT: B 250 GLU cc_start: 0.8880 (pt0) cc_final: 0.8655 (pt0) REVERT: B 319 TYR cc_start: 0.9069 (m-80) cc_final: 0.8786 (m-80) REVERT: B 323 GLU cc_start: 0.8780 (tp30) cc_final: 0.8100 (tp30) REVERT: C 236 MET cc_start: 0.9429 (mmp) cc_final: 0.9188 (mmt) REVERT: C 250 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: C 323 GLU cc_start: 0.8760 (tp30) cc_final: 0.8140 (tp30) outliers start: 22 outliers final: 13 residues processed: 193 average time/residue: 0.2667 time to fit residues: 68.5752 Evaluate side-chains 186 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.066487 restraints weight = 20271.262| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.52 r_work: 0.2751 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10269 Z= 0.244 Angle : 0.556 8.235 14010 Z= 0.293 Chirality : 0.046 0.145 1653 Planarity : 0.003 0.026 1815 Dihedral : 4.905 17.725 1365 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.92 % Allowed : 10.99 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1275 helix: -2.63 (0.76), residues: 36 sheet: -0.61 (0.24), residues: 462 loop : -0.01 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 296 HIS 0.001 0.000 HIS A 266 PHE 0.023 0.002 PHE F 301 TYR 0.015 0.002 TYR E 149 ARG 0.004 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8151 (tp30) cc_final: 0.7682 (tp30) REVERT: A 250 GLU cc_start: 0.8863 (pt0) cc_final: 0.8524 (pt0) REVERT: A 291 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8084 (ttm-80) REVERT: A 319 TYR cc_start: 0.8709 (m-80) cc_final: 0.8499 (m-80) REVERT: A 323 GLU cc_start: 0.8910 (tp30) cc_final: 0.8181 (tp30) REVERT: D 112 GLN cc_start: 0.8483 (pm20) cc_final: 0.8215 (pm20) REVERT: D 143 LEU cc_start: 0.8361 (pt) cc_final: 0.8002 (tp) REVERT: D 210 GLN cc_start: 0.8837 (mp10) cc_final: 0.8433 (mp10) REVERT: D 271 TYR cc_start: 0.6921 (m-80) cc_final: 0.6580 (m-80) REVERT: F 112 GLN cc_start: 0.8459 (pm20) cc_final: 0.8196 (pm20) REVERT: F 210 GLN cc_start: 0.8536 (mp10) cc_final: 0.7983 (mp10) REVERT: B 181 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8938 (t0) REVERT: B 250 GLU cc_start: 0.8896 (pt0) cc_final: 0.8654 (pt0) REVERT: B 291 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8231 (ttm-80) REVERT: B 323 GLU cc_start: 0.8802 (tp30) cc_final: 0.8146 (tp30) REVERT: C 236 MET cc_start: 0.9430 (mmp) cc_final: 0.9193 (mmt) REVERT: C 250 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: C 276 MET cc_start: 0.8562 (ttm) cc_final: 0.8181 (ttm) REVERT: C 319 TYR cc_start: 0.8761 (m-80) cc_final: 0.8476 (m-80) REVERT: C 323 GLU cc_start: 0.8776 (tp30) cc_final: 0.8197 (tp30) outliers start: 22 outliers final: 16 residues processed: 187 average time/residue: 0.2666 time to fit residues: 66.8427 Evaluate side-chains 186 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** F 238 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 = 0.3499 r_free = 0.3499 target = 0.099043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.064462 restraints weight = 20621.053| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.49 r_work: 0.2712 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10269 Z= 0.365 Angle : 0.600 8.434 14010 Z= 0.316 Chirality : 0.047 0.149 1653 Planarity : 0.003 0.026 1815 Dihedral : 5.131 20.489 1365 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.92 % Allowed : 11.69 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1275 helix: -3.53 (0.56), residues: 54 sheet: -0.69 (0.24), residues: 456 loop : -0.13 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 296 HIS 0.002 0.001 HIS A 266 PHE 0.024 0.002 PHE F 301 TYR 0.016 0.002 TYR E 149 ARG 0.004 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8300 (tp30) cc_final: 0.7387 (tp30) REVERT: A 276 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8349 (mtp) REVERT: A 291 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.7955 (ttm-80) REVERT: A 323 GLU cc_start: 0.8930 (tp30) cc_final: 0.8122 (tp30) REVERT: D 143 LEU cc_start: 0.8342 (pt) cc_final: 0.8049 (tp) REVERT: D 271 TYR cc_start: 0.7066 (m-80) cc_final: 0.6719 (m-80) REVERT: D 319 TYR cc_start: 0.9377 (t80) cc_final: 0.9068 (t80) REVERT: F 112 GLN cc_start: 0.8389 (pm20) cc_final: 0.8085 (pm20) REVERT: F 210 GLN cc_start: 0.8482 (mp10) cc_final: 0.7910 (mp10) REVERT: B 181 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8953 (t0) REVERT: B 250 GLU cc_start: 0.8942 (pt0) cc_final: 0.8702 (pt0) REVERT: B 323 GLU cc_start: 0.8871 (tp30) cc_final: 0.8150 (tp30) REVERT: C 250 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: C 276 MET cc_start: 0.8582 (mtm) cc_final: 0.8120 (ttm) REVERT: C 323 GLU cc_start: 0.8875 (tp30) cc_final: 0.8222 (tp30) outliers start: 22 outliers final: 16 residues processed: 186 average time/residue: 0.2593 time to fit residues: 64.9773 Evaluate side-chains 191 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.103119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.068648 restraints weight = 20140.288| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.51 r_work: 0.2792 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10269 Z= 0.158 Angle : 0.553 8.641 14010 Z= 0.290 Chirality : 0.045 0.148 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.669 18.860 1365 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.05 % Allowed : 12.74 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1275 helix: -2.50 (0.79), residues: 36 sheet: -0.62 (0.24), residues: 462 loop : -0.03 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 296 HIS 0.001 0.000 HIS E 183 PHE 0.020 0.002 PHE F 301 TYR 0.013 0.001 TYR E 149 ARG 0.004 0.001 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8147 (tp30) cc_final: 0.7832 (tp30) REVERT: A 250 GLU cc_start: 0.8874 (pt0) cc_final: 0.8459 (pt0) REVERT: A 291 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8180 (ttm-80) REVERT: A 323 GLU cc_start: 0.8848 (tp30) cc_final: 0.8118 (tp30) REVERT: D 112 GLN cc_start: 0.8502 (pm20) cc_final: 0.8240 (pm20) REVERT: D 143 LEU cc_start: 0.8344 (pt) cc_final: 0.8045 (tp) REVERT: D 210 GLN cc_start: 0.8862 (mp10) cc_final: 0.8489 (mp10) REVERT: D 226 LYS cc_start: 0.5766 (tttt) cc_final: 0.5545 (tttp) REVERT: D 271 TYR cc_start: 0.7039 (m-80) cc_final: 0.6756 (m-80) REVERT: E 210 GLN cc_start: 0.8378 (mp10) cc_final: 0.7992 (mp10) REVERT: F 112 GLN cc_start: 0.8441 (pm20) cc_final: 0.8169 (pm20) REVERT: F 143 LEU cc_start: 0.8304 (pt) cc_final: 0.7936 (tp) REVERT: F 210 GLN cc_start: 0.8605 (mp10) cc_final: 0.8050 (mp10) REVERT: B 250 GLU cc_start: 0.8882 (pt0) cc_final: 0.8663 (pt0) REVERT: B 323 GLU cc_start: 0.8802 (tp30) cc_final: 0.8130 (tp30) REVERT: C 250 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8491 (pt0) REVERT: C 276 MET cc_start: 0.8506 (mtm) cc_final: 0.8184 (ttm) REVERT: C 319 TYR cc_start: 0.8639 (m-80) cc_final: 0.8395 (m-80) REVERT: C 323 GLU cc_start: 0.8775 (tp30) cc_final: 0.8123 (tp30) outliers start: 12 outliers final: 6 residues processed: 183 average time/residue: 0.2768 time to fit residues: 67.9112 Evaluate side-chains 172 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068672 restraints weight = 20140.336| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.51 r_work: 0.2797 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10269 Z= 0.174 Angle : 0.551 8.279 14010 Z= 0.288 Chirality : 0.045 0.149 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.564 17.181 1365 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 13.09 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1275 helix: -2.47 (0.78), residues: 36 sheet: -0.57 (0.24), residues: 462 loop : -0.03 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 296 HIS 0.001 0.000 HIS A 266 PHE 0.026 0.002 PHE F 301 TYR 0.013 0.001 TYR E 172 ARG 0.004 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8246 (tp30) cc_final: 0.8042 (tp30) REVERT: A 250 GLU cc_start: 0.8869 (pt0) cc_final: 0.8424 (pt0) REVERT: A 279 GLN cc_start: 0.8259 (pm20) cc_final: 0.8039 (pm20) REVERT: A 291 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: A 323 GLU cc_start: 0.8812 (tp30) cc_final: 0.8104 (tp30) REVERT: D 112 GLN cc_start: 0.8493 (pm20) cc_final: 0.8221 (pm20) REVERT: D 143 LEU cc_start: 0.8387 (pt) cc_final: 0.8091 (tp) REVERT: D 210 GLN cc_start: 0.8871 (mp10) cc_final: 0.8501 (mp10) REVERT: D 226 LYS cc_start: 0.5720 (tttt) cc_final: 0.5223 (tttp) REVERT: D 271 TYR cc_start: 0.7008 (m-80) cc_final: 0.6740 (m-80) REVERT: E 210 GLN cc_start: 0.8432 (mp10) cc_final: 0.8032 (mp10) REVERT: F 112 GLN cc_start: 0.8446 (pm20) cc_final: 0.8166 (pm20) REVERT: F 143 LEU cc_start: 0.8383 (pt) cc_final: 0.7998 (tp) REVERT: F 210 GLN cc_start: 0.8631 (mp10) cc_final: 0.8086 (mp10) REVERT: B 250 GLU cc_start: 0.8877 (pt0) cc_final: 0.8673 (pt0) REVERT: B 323 GLU cc_start: 0.8734 (tp30) cc_final: 0.8100 (tp30) REVERT: C 250 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8460 (pt0) REVERT: C 276 MET cc_start: 0.8481 (mtm) cc_final: 0.8032 (ttm) REVERT: C 291 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8357 (ttm-80) REVERT: C 323 GLU cc_start: 0.8693 (tp30) cc_final: 0.8101 (tp30) outliers start: 11 outliers final: 6 residues processed: 181 average time/residue: 0.2639 time to fit residues: 63.7729 Evaluate side-chains 177 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065428 restraints weight = 20257.367| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.43 r_work: 0.2742 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10269 Z= 0.347 Angle : 0.638 10.989 14010 Z= 0.331 Chirality : 0.048 0.356 1653 Planarity : 0.003 0.026 1815 Dihedral : 4.920 19.498 1365 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.05 % Allowed : 13.70 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1275 helix: -2.43 (0.80), residues: 36 sheet: -0.58 (0.24), residues: 462 loop : -0.09 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 296 HIS 0.002 0.001 HIS A 266 PHE 0.026 0.002 PHE F 301 TYR 0.014 0.002 TYR E 172 ARG 0.007 0.001 ARG B 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8273 (tp30) cc_final: 0.7377 (tp30) REVERT: A 250 GLU cc_start: 0.8885 (pt0) cc_final: 0.8523 (pt0) REVERT: A 291 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.7953 (ttm-80) REVERT: A 323 GLU cc_start: 0.8842 (tp30) cc_final: 0.8088 (tp30) REVERT: D 143 LEU cc_start: 0.8389 (pt) cc_final: 0.8087 (tp) REVERT: D 210 GLN cc_start: 0.8824 (mp10) cc_final: 0.8412 (mp10) REVERT: D 271 TYR cc_start: 0.7123 (m-80) cc_final: 0.6831 (m-80) REVERT: E 193 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7327 (tpp80) REVERT: F 112 GLN cc_start: 0.8411 (pm20) cc_final: 0.8123 (pm20) REVERT: F 210 GLN cc_start: 0.8564 (mp10) cc_final: 0.7993 (mp10) REVERT: B 250 GLU cc_start: 0.8898 (pt0) cc_final: 0.8679 (pt0) REVERT: B 323 GLU cc_start: 0.8785 (tp30) cc_final: 0.8108 (tp30) REVERT: C 250 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8520 (pt0) REVERT: C 276 MET cc_start: 0.8525 (mtm) cc_final: 0.8202 (ttm) REVERT: C 323 GLU cc_start: 0.8794 (tp30) cc_final: 0.8162 (tp30) outliers start: 12 outliers final: 10 residues processed: 178 average time/residue: 0.2751 time to fit residues: 65.6265 Evaluate side-chains 177 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 250 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067791 restraints weight = 19974.945| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.51 r_work: 0.2782 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10269 Z= 0.196 Angle : 0.588 10.126 14010 Z= 0.306 Chirality : 0.046 0.300 1653 Planarity : 0.003 0.029 1815 Dihedral : 4.721 17.373 1365 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.22 % Allowed : 13.26 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1275 helix: -2.39 (0.80), residues: 36 sheet: -0.60 (0.24), residues: 462 loop : -0.14 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 296 HIS 0.001 0.000 HIS F 183 PHE 0.025 0.002 PHE F 301 TYR 0.013 0.001 TYR E 172 ARG 0.005 0.001 ARG E 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5308.99 seconds wall clock time: 95 minutes 32.75 seconds (5732.75 seconds total)