Starting phenix.real_space_refine on Thu Jun 4 19:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rig_53994/06_2026/9rig_53994_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rig_53994/06_2026/9rig_53994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rig_53994/06_2026/9rig_53994_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rig_53994/06_2026/9rig_53994_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rig_53994/06_2026/9rig_53994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rig_53994/06_2026/9rig_53994.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 5299 2.51 5 N 1395 2.21 5 O 1611 1.98 5 H 6321 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14669 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4515 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain: "B" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3728 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 226} Chain: "C" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3708 Classifications: {'peptide': 242} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 223} Chain: "H" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1042 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "L" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 781 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 874 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.09, per 1000 atoms: 0.21 Number of scatterers: 14669 At special positions: 0 Unit cell: (98.55, 112.05, 106.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 1611 8.00 N 1395 7.00 C 5299 6.00 H 6321 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.28 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " distance=2.08 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.12 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: 1.28 Conformation dependent library (CDL) restraints added in 492.4 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 17 sheets defined 15.3% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.826A pdb=" N SER A 10 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.677A pdb=" N MET A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.679A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 215 through 222 removed outlier: 4.831A pdb=" N LEU A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.623A pdb=" N ASP B 156 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 157 " --> pdb=" O GLY B 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 157' Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 171 through 178 removed outlier: 4.441A pdb=" N THR B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.588A pdb=" N TYR C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.853A pdb=" N LEU C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 50 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 95 removed outlier: 5.907A pdb=" N LEU A 89 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET A 253 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 258 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 130 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA A 260 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 128 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 262 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE A 126 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 22 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 removed outlier: 4.996A pdb=" N PHE A 126 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 262 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 128 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA A 260 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 130 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 258 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 260 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 106 through 110 Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.539A pdb=" N ILE B 32 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS B 99 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY B 247 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 101 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE B 245 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 103 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER B 243 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 232 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU B 70 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE B 234 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 68 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 236 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.671A pdb=" N ILE C 196 " --> pdb=" O CYS C 83 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL C 85 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 194 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 178 through 179 removed outlier: 6.270A pdb=" N TYR C 108 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS C 229 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.325A pdb=" N TRP H 36 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.973A pdb=" N CYS H 97 " --> pdb=" O TRP H 124 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP H 124 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG H 99 " --> pdb=" O ASP H 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.718A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.718A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 23 284 hydrogen bonds defined for protein. 627 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: 3.18 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6306 1.04 - 1.24: 1049 1.24 - 1.44: 2707 1.44 - 1.64: 4764 1.64 - 1.84: 65 Bond restraints: 14891 Sorted by residual: bond pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 1.334 1.468 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C ASP H 122 " pdb=" O ASP H 122 " ideal model delta sigma weight residual 1.233 1.284 -0.050 1.32e-02 5.74e+03 1.46e+01 bond pdb=" CA SER L 71 " pdb=" CB SER L 71 " ideal model delta sigma weight residual 1.535 1.472 0.063 1.71e-02 3.42e+03 1.37e+01 bond pdb=" ND1 HIS H 100 " pdb=" CE1 HIS H 100 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" NE ARG L 62 " pdb=" CZ ARG L 62 " ideal model delta sigma weight residual 1.326 1.288 0.038 1.10e-02 8.26e+03 1.19e+01 ... (remaining 14886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 25576 2.23 - 4.46: 406 4.46 - 6.69: 49 6.69 - 8.92: 5 8.92 - 11.15: 4 Bond angle restraints: 26040 Sorted by residual: angle pdb=" CA ASP H 122 " pdb=" CB ASP H 122 " pdb=" CG ASP H 122 " ideal model delta sigma weight residual 112.60 120.03 -7.43 1.00e+00 1.00e+00 5.51e+01 angle pdb=" CA ASP L 61 " pdb=" CB ASP L 61 " pdb=" CG ASP L 61 " ideal model delta sigma weight residual 112.60 118.89 -6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" C ASP H 122 " pdb=" CA ASP H 122 " pdb=" CB ASP H 122 " ideal model delta sigma weight residual 111.65 120.69 -9.04 1.44e+00 4.82e-01 3.94e+01 angle pdb=" N LEU L 4 " pdb=" CA LEU L 4 " pdb=" CB LEU L 4 " ideal model delta sigma weight residual 110.43 120.19 -9.76 1.63e+00 3.76e-01 3.58e+01 angle pdb=" CB ARG H 32 " pdb=" CG ARG H 32 " pdb=" CD ARG H 32 " ideal model delta sigma weight residual 111.30 122.45 -11.15 2.30e+00 1.89e-01 2.35e+01 ... (remaining 26035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 6820 15.39 - 30.79: 374 30.79 - 46.18: 119 46.18 - 61.57: 58 61.57 - 76.96: 11 Dihedral angle restraints: 7382 sinusoidal: 3792 harmonic: 3590 Sorted by residual: dihedral pdb=" C ASP H 122 " pdb=" N ASP H 122 " pdb=" CA ASP H 122 " pdb=" CB ASP H 122 " ideal model delta harmonic sigma weight residual -122.60 -136.65 14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" N LEU L 4 " pdb=" C LEU L 4 " pdb=" CA LEU L 4 " pdb=" CB LEU L 4 " ideal model delta harmonic sigma weight residual 122.80 134.65 -11.85 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CA LEU H 84 " pdb=" C LEU H 84 " pdb=" N THR H 85 " pdb=" CA THR H 85 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 7379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1127 0.099 - 0.199: 156 0.199 - 0.298: 19 0.298 - 0.397: 3 0.397 - 0.497: 3 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CG LEU L 4 " pdb=" CB LEU L 4 " pdb=" CD1 LEU L 4 " pdb=" CD2 LEU L 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CG LEU H 4 " pdb=" CB LEU H 4 " pdb=" CD1 LEU H 4 " pdb=" CD2 LEU H 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA ASP H 122 " pdb=" N ASP H 122 " pdb=" C ASP H 122 " pdb=" CB ASP H 122 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1305 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 37 " 0.101 2.00e-02 2.50e+03 5.15e-02 5.30e+01 pdb=" CG TYR L 37 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR L 37 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR L 37 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR L 37 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR L 37 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR L 37 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 37 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 49 " -0.085 2.00e-02 2.50e+03 4.26e-02 4.54e+01 pdb=" CG TRP H 49 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP H 49 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 49 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP H 49 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 49 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP H 49 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 49 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 49 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 49 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 55 " -0.082 2.00e-02 2.50e+03 4.28e-02 3.67e+01 pdb=" CG TYR H 55 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR H 55 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 55 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR H 55 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR H 55 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 55 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR H 55 " -0.042 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 197 2.07 - 2.70: 20857 2.70 - 3.34: 38991 3.34 - 3.97: 52850 3.97 - 4.60: 81386 Nonbonded interactions: 194281 Sorted by model distance: nonbonded pdb=" OD1 ASN D 31 " pdb=" H TYR D 33 " model vdw 1.441 2.450 nonbonded pdb=" OE1 GLU A 61 " pdb=" H GLU A 61 " model vdw 1.551 2.450 nonbonded pdb=" OE1 GLU A 51 " pdb=" H GLU A 51 " model vdw 1.556 2.450 nonbonded pdb=" OD2 ASP B 204 " pdb=" HD1 HIS B 209 " model vdw 1.565 2.450 nonbonded pdb=" O TYR C 107 " pdb=" H LYS C 230 " model vdw 1.576 2.450 ... (remaining 194276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.008 0.247 8573 Z= 0.452 Angle : 0.905 11.150 11711 Z= 0.540 Chirality : 0.068 0.497 1308 Planarity : 0.008 0.104 1515 Dihedral : 10.734 76.964 3073 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.44 % Allowed : 4.14 % Favored : 95.42 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1070 helix: -3.21 (0.48), residues: 69 sheet: -0.18 (0.29), residues: 300 loop : -0.47 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG H 99 TYR 0.101 0.007 TYR L 37 PHE 0.020 0.002 PHE H 80 TRP 0.085 0.007 TRP H 49 HIS 0.010 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.43 ( 8570) covalent geometry : angle 0.90294 / 0.54 (11705) SS BOND : bond 0.15439 / 8.06 ( 3) SS BOND : angle 3.01719 / 1.75 ( 6) hydrogen bonds : bond 0.20469 / 14.39 ( 251) hydrogen bonds : angle 8.53802 / 6.01 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.9094 (m) cc_final: 0.8507 (p) REVERT: A 192 VAL cc_start: 0.9460 (t) cc_final: 0.9144 (m) REVERT: A 199 SER cc_start: 0.8930 (m) cc_final: 0.8565 (t) REVERT: A 206 ASP cc_start: 0.7788 (t0) cc_final: 0.7564 (t70) REVERT: A 227 ASN cc_start: 0.8588 (m-40) cc_final: 0.8154 (m-40) REVERT: A 234 SER cc_start: 0.8895 (p) cc_final: 0.8654 (p) REVERT: A 266 MET cc_start: 0.8401 (mtp) cc_final: 0.7976 (mtp) REVERT: B 37 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7893 (tt0) REVERT: B 76 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8320 (mttp) REVERT: B 139 THR cc_start: 0.8183 (p) cc_final: 0.7759 (p) REVERT: B 175 LEU cc_start: 0.9626 (tp) cc_final: 0.9352 (tp) REVERT: B 186 ARG cc_start: 0.8663 (ptm-80) cc_final: 0.8280 (ptm160) REVERT: B 223 ASP cc_start: 0.8045 (t0) cc_final: 0.7689 (t0) REVERT: B 236 ILE cc_start: 0.9327 (mp) cc_final: 0.8788 (pt) REVERT: C 7 LYS cc_start: 0.9161 (mmtt) cc_final: 0.7943 (mptt) REVERT: C 18 ASP cc_start: 0.8377 (t70) cc_final: 0.8040 (t0) REVERT: C 42 ASN cc_start: 0.8760 (t0) cc_final: 0.8533 (t0) REVERT: C 47 CYS cc_start: 0.8780 (m) cc_final: 0.8353 (m) REVERT: C 56 ASN cc_start: 0.8950 (t0) cc_final: 0.8484 (t0) REVERT: C 187 ASP cc_start: 0.9010 (t0) cc_final: 0.8717 (t0) REVERT: C 230 LYS cc_start: 0.8255 (pttp) cc_final: 0.6837 (tttt) REVERT: H 56 SER cc_start: 0.6400 (p) cc_final: 0.6170 (t) REVERT: H 76 SER cc_start: 0.5511 (p) cc_final: 0.4857 (m) REVERT: D 35 ASP cc_start: 0.8401 (m-30) cc_final: 0.8195 (m-30) REVERT: D 59 ASP cc_start: 0.7764 (m-30) cc_final: 0.7248 (m-30) REVERT: D 64 MET cc_start: 0.7554 (mmt) cc_final: 0.7154 (mmt) outliers start: 4 outliers final: 2 residues processed: 274 average time/residue: 0.1766 time to fit residues: 66.4449 Evaluate side-chains 171 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain D residue 17 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** C 180 HIS ** 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 = 0.3744 r_free = 0.3744 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113001 restraints weight = 39876.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116692 restraints weight = 15327.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118984 restraints weight = 8143.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120352 restraints weight = 5388.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121034 restraints weight = 4208.849| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8573 Z= 0.163 Angle : 0.569 5.579 11711 Z= 0.296 Chirality : 0.044 0.165 1308 Planarity : 0.004 0.034 1515 Dihedral : 5.862 59.357 1191 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.20 % Allowed : 10.47 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1070 helix: -2.63 (0.49), residues: 76 sheet: -0.08 (0.29), residues: 307 loop : -0.44 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.018 0.001 TYR B 100 PHE 0.011 0.001 PHE B 82 TRP 0.016 0.001 TRP H 49 HIS 0.006 0.001 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 8570) covalent geometry : angle 0.56885 / 0.30 (11705) SS BOND : bond 0.00117 / 0.06 ( 3) SS BOND : angle 1.00220 / 0.51 ( 6) hydrogen bonds : bond 0.04387 / 3.14 ( 251) hydrogen bonds : angle 6.67023 / 4.73 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8105 (m-30) cc_final: 0.7615 (m-30) REVERT: A 82 SER cc_start: 0.9072 (m) cc_final: 0.8549 (p) REVERT: A 199 SER cc_start: 0.9120 (m) cc_final: 0.8850 (t) REVERT: B 67 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6144 (m-30) REVERT: B 76 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8444 (mttp) REVERT: B 223 ASP cc_start: 0.8085 (t0) cc_final: 0.7803 (t0) REVERT: C 7 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8055 (mptt) REVERT: C 18 ASP cc_start: 0.8040 (t70) cc_final: 0.7836 (t0) REVERT: C 47 CYS cc_start: 0.8435 (m) cc_final: 0.7961 (m) REVERT: C 56 ASN cc_start: 0.8925 (t0) cc_final: 0.8527 (t0) REVERT: C 187 ASP cc_start: 0.9085 (t0) cc_final: 0.8747 (t0) REVERT: C 228 LEU cc_start: 0.8758 (tt) cc_final: 0.8499 (tp) REVERT: H 62 SER cc_start: 0.3446 (t) cc_final: 0.3178 (m) REVERT: D 59 ASP cc_start: 0.7308 (m-30) cc_final: 0.6984 (m-30) REVERT: D 64 MET cc_start: 0.7247 (mmt) cc_final: 0.6961 (mmt) outliers start: 11 outliers final: 8 residues processed: 197 average time/residue: 0.1761 time to fit residues: 48.1993 Evaluate side-chains 166 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 82 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 83 optimal weight: 40.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 211 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113112 restraints weight = 40519.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116776 restraints weight = 15609.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118954 restraints weight = 8277.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120303 restraints weight = 5533.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120982 restraints weight = 4332.972| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8573 Z= 0.145 Angle : 0.538 5.577 11711 Z= 0.275 Chirality : 0.043 0.157 1308 Planarity : 0.004 0.033 1515 Dihedral : 5.548 51.729 1189 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.42 % Allowed : 12.00 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1070 helix: -2.45 (0.52), residues: 76 sheet: -0.16 (0.30), residues: 302 loop : -0.54 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.014 0.001 TYR C 108 PHE 0.016 0.001 PHE A 126 TRP 0.013 0.001 TRP H 49 HIS 0.004 0.001 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8570) covalent geometry : angle 0.53797 / 0.27 (11705) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 0.74847 / 0.40 ( 6) hydrogen bonds : bond 0.03659 / 2.55 ( 251) hydrogen bonds : angle 6.25102 / 4.42 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.9076 (m) cc_final: 0.8538 (p) REVERT: A 124 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8513 (mm-30) REVERT: A 183 LEU cc_start: 0.9131 (mp) cc_final: 0.8916 (mt) REVERT: A 199 SER cc_start: 0.9106 (m) cc_final: 0.8871 (t) REVERT: B 67 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6243 (m-30) REVERT: B 76 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8496 (mttp) REVERT: B 223 ASP cc_start: 0.8149 (t0) cc_final: 0.7851 (t0) REVERT: C 7 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8036 (mptt) REVERT: C 47 CYS cc_start: 0.8496 (m) cc_final: 0.7974 (m) REVERT: C 56 ASN cc_start: 0.8915 (t0) cc_final: 0.8586 (t0) REVERT: C 177 TYR cc_start: 0.9068 (m-80) cc_final: 0.8862 (m-80) REVERT: C 187 ASP cc_start: 0.9143 (t0) cc_final: 0.8805 (t0) REVERT: H 19 SER cc_start: 0.7261 (m) cc_final: 0.6828 (p) REVERT: D 59 ASP cc_start: 0.7385 (m-30) cc_final: 0.7010 (m-30) REVERT: D 64 MET cc_start: 0.7269 (mmt) cc_final: 0.6974 (mmt) outliers start: 13 outliers final: 9 residues processed: 168 average time/residue: 0.1767 time to fit residues: 41.3053 Evaluate side-chains 161 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112361 restraints weight = 40406.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115891 restraints weight = 15464.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118043 restraints weight = 8212.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119350 restraints weight = 5469.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119899 restraints weight = 4284.996| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8573 Z= 0.203 Angle : 0.555 5.837 11711 Z= 0.284 Chirality : 0.043 0.154 1308 Planarity : 0.004 0.051 1515 Dihedral : 5.404 44.102 1189 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.29 % Allowed : 11.34 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.25), residues: 1070 helix: -2.34 (0.54), residues: 76 sheet: -0.21 (0.30), residues: 301 loop : -0.73 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 3 TYR 0.018 0.002 TYR H 115 PHE 0.011 0.001 PHE A 126 TRP 0.013 0.001 TRP H 49 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 8570) covalent geometry : angle 0.55472 / 0.28 (11705) SS BOND : bond 0.00253 / 0.12 ( 3) SS BOND : angle 1.02536 / 0.55 ( 6) hydrogen bonds : bond 0.03422 / 2.34 ( 251) hydrogen bonds : angle 6.11534 / 4.31 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.9070 (m) cc_final: 0.8597 (p) REVERT: A 154 MET cc_start: 0.7374 (ttp) cc_final: 0.7150 (ttp) REVERT: A 199 SER cc_start: 0.9017 (m) cc_final: 0.8802 (t) REVERT: A 266 MET cc_start: 0.8465 (mtp) cc_final: 0.8182 (mtp) REVERT: B 67 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6514 (m-30) REVERT: B 76 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8421 (mttp) REVERT: B 197 TYR cc_start: 0.8647 (t80) cc_final: 0.8419 (t80) REVERT: C 7 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8053 (mptt) REVERT: C 47 CYS cc_start: 0.8488 (m) cc_final: 0.8043 (m) REVERT: C 56 ASN cc_start: 0.9056 (t0) cc_final: 0.8731 (t0) REVERT: C 177 TYR cc_start: 0.9140 (m-80) cc_final: 0.8856 (m-80) REVERT: C 187 ASP cc_start: 0.9157 (t0) cc_final: 0.8824 (t0) REVERT: H 19 SER cc_start: 0.7475 (m) cc_final: 0.7039 (p) REVERT: D 59 ASP cc_start: 0.7485 (m-30) cc_final: 0.7107 (m-30) REVERT: D 64 MET cc_start: 0.6941 (mmt) cc_final: 0.6596 (mmt) outliers start: 21 outliers final: 15 residues processed: 168 average time/residue: 0.1672 time to fit residues: 39.5219 Evaluate side-chains 157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain D residue 17 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 0.0030 chunk 90 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113765 restraints weight = 40385.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117375 restraints weight = 15488.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119522 restraints weight = 8168.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120821 restraints weight = 5443.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121366 restraints weight = 4284.105| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8573 Z= 0.117 Angle : 0.507 5.055 11711 Z= 0.257 Chirality : 0.043 0.151 1308 Planarity : 0.004 0.031 1515 Dihedral : 5.046 40.370 1189 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.64 % Allowed : 12.43 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1070 helix: -2.23 (0.53), residues: 77 sheet: -0.18 (0.30), residues: 300 loop : -0.63 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.020 0.001 TYR C 108 PHE 0.013 0.001 PHE A 126 TRP 0.008 0.001 TRP L 36 HIS 0.002 0.001 HIS H 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8570) covalent geometry : angle 0.50678 / 0.26 (11705) SS BOND : bond 0.00142 / 0.07 ( 3) SS BOND : angle 0.66955 / 0.38 ( 6) hydrogen bonds : bond 0.03041 / 2.08 ( 251) hydrogen bonds : angle 5.86493 / 4.15 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.9037 (m) cc_final: 0.8567 (p) REVERT: A 124 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8483 (mm-30) REVERT: B 67 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: B 76 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8412 (mttp) REVERT: B 197 TYR cc_start: 0.8744 (t80) cc_final: 0.8522 (t80) REVERT: C 7 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8042 (mptt) REVERT: C 47 CYS cc_start: 0.8505 (m) cc_final: 0.8033 (m) REVERT: C 56 ASN cc_start: 0.9052 (t0) cc_final: 0.8771 (t0) REVERT: C 177 TYR cc_start: 0.9069 (m-80) cc_final: 0.8836 (m-80) REVERT: C 187 ASP cc_start: 0.9143 (t0) cc_final: 0.8816 (t0) REVERT: H 19 SER cc_start: 0.7477 (m) cc_final: 0.6990 (p) REVERT: D 59 ASP cc_start: 0.7621 (m-30) cc_final: 0.7244 (m-30) REVERT: D 64 MET cc_start: 0.6940 (mmt) cc_final: 0.6591 (mmt) outliers start: 15 outliers final: 10 residues processed: 167 average time/residue: 0.1727 time to fit residues: 40.6996 Evaluate side-chains 158 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 79 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113135 restraints weight = 40208.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116684 restraints weight = 15536.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118828 restraints weight = 8268.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120000 restraints weight = 5528.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120778 restraints weight = 4391.625| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8573 Z= 0.161 Angle : 0.521 5.522 11711 Z= 0.264 Chirality : 0.043 0.151 1308 Planarity : 0.004 0.033 1515 Dihedral : 4.980 39.152 1189 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.07 % Allowed : 12.10 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1070 helix: -2.14 (0.55), residues: 76 sheet: -0.09 (0.31), residues: 285 loop : -0.74 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.013 0.001 TYR B 64 PHE 0.010 0.001 PHE A 126 TRP 0.009 0.001 TRP L 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 8570) covalent geometry : angle 0.52123 / 0.26 (11705) SS BOND : bond 0.00213 / 0.10 ( 3) SS BOND : angle 0.82787 / 0.45 ( 6) hydrogen bonds : bond 0.03047 / 2.07 ( 251) hydrogen bonds : angle 5.81041 / 4.12 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6672 (mtt) cc_final: 0.6168 (mtt) REVERT: A 82 SER cc_start: 0.9049 (m) cc_final: 0.8589 (p) REVERT: A 124 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: B 67 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: B 76 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8429 (mttp) REVERT: B 197 TYR cc_start: 0.8756 (t80) cc_final: 0.8552 (t80) REVERT: C 7 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8055 (mptt) REVERT: C 47 CYS cc_start: 0.8557 (m) cc_final: 0.8115 (m) REVERT: C 56 ASN cc_start: 0.9069 (t0) cc_final: 0.8814 (t0) REVERT: C 108 TYR cc_start: 0.8456 (m-80) cc_final: 0.8232 (m-10) REVERT: C 177 TYR cc_start: 0.9110 (m-80) cc_final: 0.8855 (m-80) REVERT: C 187 ASP cc_start: 0.9157 (t0) cc_final: 0.8837 (t0) REVERT: H 19 SER cc_start: 0.7305 (m) cc_final: 0.6872 (p) REVERT: D 59 ASP cc_start: 0.7688 (m-30) cc_final: 0.7285 (m-30) REVERT: D 64 MET cc_start: 0.6968 (mmt) cc_final: 0.6615 (mmt) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.1593 time to fit residues: 35.4358 Evaluate side-chains 157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111945 restraints weight = 40519.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115479 restraints weight = 15793.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117614 restraints weight = 8509.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118945 restraints weight = 5747.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119559 restraints weight = 4537.675| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8573 Z= 0.199 Angle : 0.545 5.729 11711 Z= 0.277 Chirality : 0.043 0.148 1308 Planarity : 0.004 0.035 1515 Dihedral : 5.052 38.871 1189 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.29 % Allowed : 12.54 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.25), residues: 1070 helix: -2.12 (0.55), residues: 76 sheet: -0.14 (0.30), residues: 285 loop : -0.81 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.016 0.001 TYR C 108 PHE 0.010 0.001 PHE A 126 TRP 0.010 0.001 TRP L 36 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 ( 8570) covalent geometry : angle 0.54463 / 0.28 (11705) SS BOND : bond 0.00245 / 0.12 ( 3) SS BOND : angle 0.99419 / 0.55 ( 6) hydrogen bonds : bond 0.03135 / 2.13 ( 251) hydrogen bonds : angle 5.86944 / 4.16 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.8719 (m) cc_final: 0.8166 (p) REVERT: A 124 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: B 67 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6384 (m-30) REVERT: B 76 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8415 (mttp) REVERT: C 7 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8029 (mptt) REVERT: C 47 CYS cc_start: 0.8557 (m) cc_final: 0.8113 (m) REVERT: C 56 ASN cc_start: 0.9084 (t0) cc_final: 0.8792 (t0) REVERT: C 93 ASP cc_start: 0.8731 (p0) cc_final: 0.8441 (p0) REVERT: C 177 TYR cc_start: 0.9136 (m-80) cc_final: 0.8835 (m-80) REVERT: C 187 ASP cc_start: 0.9154 (t0) cc_final: 0.8844 (t0) REVERT: H 19 SER cc_start: 0.7276 (m) cc_final: 0.7048 (p) REVERT: H 134 SER cc_start: 0.4494 (m) cc_final: 0.4293 (p) REVERT: D 59 ASP cc_start: 0.7727 (m-30) cc_final: 0.7334 (m-30) REVERT: D 64 MET cc_start: 0.6980 (mmt) cc_final: 0.6625 (mmt) outliers start: 21 outliers final: 18 residues processed: 154 average time/residue: 0.1647 time to fit residues: 35.5973 Evaluate side-chains 152 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112883 restraints weight = 40529.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116438 restraints weight = 15733.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118598 restraints weight = 8454.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119915 restraints weight = 5683.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120464 restraints weight = 4483.753| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8573 Z= 0.139 Angle : 0.514 5.451 11711 Z= 0.260 Chirality : 0.043 0.151 1308 Planarity : 0.004 0.034 1515 Dihedral : 4.891 38.869 1189 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.07 % Allowed : 13.85 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1070 helix: -2.02 (0.56), residues: 76 sheet: -0.11 (0.30), residues: 286 loop : -0.74 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.022 0.001 TYR C 108 PHE 0.010 0.001 PHE A 126 TRP 0.009 0.001 TRP L 36 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8570) covalent geometry : angle 0.51398 / 0.26 (11705) SS BOND : bond 0.00160 / 0.08 ( 3) SS BOND : angle 0.71551 / 0.40 ( 6) hydrogen bonds : bond 0.02953 / 2.00 ( 251) hydrogen bonds : angle 5.73284 / 4.06 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6633 (mtt) cc_final: 0.6130 (mtt) REVERT: A 82 SER cc_start: 0.8688 (m) cc_final: 0.8151 (p) REVERT: A 124 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8470 (mm-30) REVERT: A 218 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8739 (mmmt) REVERT: B 67 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: B 76 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8379 (mttp) REVERT: C 7 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8035 (mptt) REVERT: C 47 CYS cc_start: 0.8559 (m) cc_final: 0.8122 (m) REVERT: C 56 ASN cc_start: 0.9051 (t0) cc_final: 0.8792 (t0) REVERT: C 177 TYR cc_start: 0.9111 (m-80) cc_final: 0.8820 (m-80) REVERT: C 187 ASP cc_start: 0.9125 (t0) cc_final: 0.8841 (t0) REVERT: H 134 SER cc_start: 0.4570 (m) cc_final: 0.4362 (p) REVERT: D 59 ASP cc_start: 0.7718 (m-30) cc_final: 0.7307 (m-30) REVERT: D 64 MET cc_start: 0.6997 (mmt) cc_final: 0.6650 (mmt) outliers start: 19 outliers final: 16 residues processed: 169 average time/residue: 0.1712 time to fit residues: 40.4915 Evaluate side-chains 158 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113766 restraints weight = 40393.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117329 restraints weight = 15598.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119478 restraints weight = 8315.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120811 restraints weight = 5570.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121419 restraints weight = 4388.600| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8573 Z= 0.117 Angle : 0.501 5.045 11711 Z= 0.253 Chirality : 0.043 0.148 1308 Planarity : 0.004 0.036 1515 Dihedral : 4.717 38.796 1189 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.96 % Allowed : 14.50 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1070 helix: -1.98 (0.55), residues: 76 sheet: -0.07 (0.30), residues: 286 loop : -0.66 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.020 0.001 TYR C 108 PHE 0.010 0.001 PHE A 126 TRP 0.007 0.001 TRP L 36 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8570) covalent geometry : angle 0.50080 / 0.25 (11705) SS BOND : bond 0.00172 / 0.08 ( 3) SS BOND : angle 0.63699 / 0.37 ( 6) hydrogen bonds : bond 0.02813 / 1.90 ( 251) hydrogen bonds : angle 5.59792 / 3.98 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6599 (mtt) cc_final: 0.6090 (mtt) REVERT: A 82 SER cc_start: 0.8672 (m) cc_final: 0.8127 (p) REVERT: A 124 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8441 (mm-30) REVERT: A 218 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8729 (mmmt) REVERT: B 67 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: B 76 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8385 (mttp) REVERT: B 113 ASN cc_start: 0.8074 (p0) cc_final: 0.7832 (p0) REVERT: B 211 ASN cc_start: 0.8691 (m-40) cc_final: 0.8467 (m-40) REVERT: C 7 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8123 (mptt) REVERT: C 47 CYS cc_start: 0.8567 (m) cc_final: 0.8135 (m) REVERT: C 162 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8830 (mm110) REVERT: C 177 TYR cc_start: 0.9114 (m-80) cc_final: 0.8840 (m-80) REVERT: C 187 ASP cc_start: 0.9131 (t0) cc_final: 0.8832 (t0) REVERT: D 59 ASP cc_start: 0.7711 (m-30) cc_final: 0.7294 (m-30) REVERT: D 64 MET cc_start: 0.6998 (mmt) cc_final: 0.6667 (mmt) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.1624 time to fit residues: 36.2111 Evaluate side-chains 160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112369 restraints weight = 40349.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115849 restraints weight = 15655.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118008 restraints weight = 8430.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119272 restraints weight = 5653.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119922 restraints weight = 4457.636| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8573 Z= 0.187 Angle : 0.539 5.539 11711 Z= 0.274 Chirality : 0.043 0.145 1308 Planarity : 0.004 0.030 1515 Dihedral : 4.868 38.273 1189 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.29 % Allowed : 14.39 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.25), residues: 1070 helix: -1.98 (0.56), residues: 76 sheet: -0.16 (0.30), residues: 285 loop : -0.81 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.020 0.002 TYR C 108 PHE 0.009 0.001 PHE A 126 TRP 0.010 0.001 TRP L 36 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 8570) covalent geometry : angle 0.53883 / 0.27 (11705) SS BOND : bond 0.00225 / 0.11 ( 3) SS BOND : angle 0.95550 / 0.52 ( 6) hydrogen bonds : bond 0.03032 / 2.05 ( 251) hydrogen bonds : angle 5.72771 / 4.06 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6871 (mtt) cc_final: 0.6352 (mtt) REVERT: A 82 SER cc_start: 0.8620 (m) cc_final: 0.8067 (p) REVERT: A 124 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8490 (mm-30) REVERT: A 218 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8690 (mmmt) REVERT: B 67 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: B 76 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8400 (mttp) REVERT: B 211 ASN cc_start: 0.8718 (m-40) cc_final: 0.8462 (t0) REVERT: C 7 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8109 (mptt) REVERT: C 47 CYS cc_start: 0.8558 (m) cc_final: 0.8168 (m) REVERT: C 162 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8854 (mm110) REVERT: C 164 SER cc_start: 0.8843 (m) cc_final: 0.8278 (p) REVERT: C 177 TYR cc_start: 0.9133 (m-80) cc_final: 0.8800 (m-80) REVERT: C 187 ASP cc_start: 0.9142 (t0) cc_final: 0.8846 (t0) REVERT: D 64 MET cc_start: 0.7003 (mmt) cc_final: 0.6674 (mmt) outliers start: 21 outliers final: 17 residues processed: 157 average time/residue: 0.1688 time to fit residues: 37.3228 Evaluate side-chains 157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111328 restraints weight = 40735.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114770 restraints weight = 15946.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116910 restraints weight = 8572.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117995 restraints weight = 5727.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118858 restraints weight = 4582.578| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8573 Z= 0.281 Angle : 0.612 5.810 11711 Z= 0.316 Chirality : 0.045 0.147 1308 Planarity : 0.004 0.040 1515 Dihedral : 5.376 40.654 1189 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.73 % Allowed : 14.18 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1070 helix: -2.16 (0.54), residues: 76 sheet: -0.29 (0.30), residues: 289 loop : -1.07 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.025 0.002 TYR C 108 PHE 0.014 0.002 PHE B 106 TRP 0.013 0.002 TRP L 36 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 ( 8570) covalent geometry : angle 0.61113 / 0.32 (11705) SS BOND : bond 0.00298 / 0.14 ( 3) SS BOND : angle 1.23706 / 0.68 ( 6) hydrogen bonds : bond 0.03376 / 2.29 ( 251) hydrogen bonds : angle 6.03278 / 4.26 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2664.42 seconds wall clock time: 46 minutes 22.97 seconds (2782.97 seconds total)