Starting phenix.real_space_refine on Wed Jun 3 13:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21av_67541/06_2026/21av_67541.cif Found real_map, /net/cci-nas-00/data/ceres_data/21av_67541/06_2026/21av_67541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21av_67541/06_2026/21av_67541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21av_67541/06_2026/21av_67541.map" model { file = "/net/cci-nas-00/data/ceres_data/21av_67541/06_2026/21av_67541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21av_67541/06_2026/21av_67541.cif" } resolution = 2.69 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= -0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 3806 2.51 5 N 1042 2.21 5 O 1220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s 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: 6113 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2467 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302} Chain: "A" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 928 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.72, per 1000 atoms: 0.28 Number of scatterers: 6113 At special positions: 0 Unit cell: (70.3, 107.35, 108.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1220 8.00 N 1042 7.00 C 3806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 80 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 156 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 327 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 266 " distance=2.05 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 305 " distance=2.06 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 303 " distance=2.03 Simple disulfide: pdb=" SG CYS H 274 " - pdb=" SG CYS H 280 " distance=2.03 Simple disulfide: pdb=" SG CYS H 287 " - pdb=" SG CYS H 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG E 1 " - " ASN D 25 " " NAG F 1 " - " ASN H 63 " " NAG G 1 " - " ASN H 33 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 300.6 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 20 sheets defined 13.9% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.858A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.860A pdb=" N GLU D 84 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 53 removed outlier: 3.530A pdb=" N ARG H 53 " --> pdb=" O CYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 76 through 80 removed outlier: 3.597A pdb=" N VAL H 80 " --> pdb=" O ARG H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 187 through 199 Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 267 through 278 removed outlier: 3.646A pdb=" N GLY H 278 " --> pdb=" O CYS H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 290 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.564A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.790A pdb=" N THR A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.544A pdb=" N SER B 29 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.811A pdb=" N GLU B 82 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.611A pdb=" N LEU C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.976A pdb=" N TRP C 33 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.502A pdb=" N CYS C 96 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP C 115 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG C 98 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 111 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP C 102 " --> pdb=" O TRP C 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.549A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.588A pdb=" N ALA D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 23 removed outlier: 3.601A pdb=" N SER D 71 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 70 through 71 removed outlier: 6.814A pdb=" N TYR H 70 " --> pdb=" O LEU H 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.537A pdb=" N PHE H 129 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE H 175 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU H 131 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 147 through 149 Processing sheet with id=AB1, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.972A pdb=" N LYS H 207 " --> pdb=" O THR H 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.568A pdb=" N CYS H 327 " --> pdb=" O ASP H 231 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER H 331 " --> pdb=" O VAL H 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA H 228 " --> pdb=" O MET H 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 244 through 248 Processing sheet with id=AB4, first strand: chain 'H' and resid 256 through 257 Processing sheet with id=AB5, first strand: chain 'H' and resid 259 through 260 Processing sheet with id=AB6, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.927A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.927A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS A 112 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.719A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AC2, first strand: chain 'B' and resid 18 through 23 removed outlier: 3.502A pdb=" N THR B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2002 1.36 - 1.49: 1714 1.49 - 1.63: 2477 1.63 - 1.76: 0 1.76 - 1.89: 61 Bond restraints: 6254 Sorted by residual: bond pdb=" CB CYS H 305 " pdb=" SG CYS H 305 " ideal model delta sigma weight residual 1.808 1.891 -0.083 3.30e-02 9.18e+02 6.37e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" CB CYS C 21 " pdb=" SG CYS C 21 " ideal model delta sigma weight residual 1.808 1.859 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 6249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 8417 2.81 - 5.62: 51 5.62 - 8.43: 7 8.43 - 11.25: 1 11.25 - 14.06: 1 Bond angle restraints: 8477 Sorted by residual: angle pdb=" CA CYS H 258 " pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " ideal model delta sigma weight residual 114.40 128.46 -14.06 2.30e+00 1.89e-01 3.74e+01 angle pdb=" CA CYS H 266 " pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " ideal model delta sigma weight residual 114.40 124.20 -9.80 2.30e+00 1.89e-01 1.82e+01 angle pdb=" N CYS H 258 " pdb=" CA CYS H 258 " pdb=" C CYS H 258 " ideal model delta sigma weight residual 108.74 113.64 -4.90 1.38e+00 5.25e-01 1.26e+01 angle pdb=" CA CYS C 80 " pdb=" CB CYS C 80 " pdb=" SG CYS C 80 " ideal model delta sigma weight residual 114.40 122.41 -8.01 2.30e+00 1.89e-01 1.21e+01 angle pdb=" C ASP D 51 " pdb=" CA ASP D 51 " pdb=" CB ASP D 51 " ideal model delta sigma weight residual 110.42 116.19 -5.77 1.99e+00 2.53e-01 8.40e+00 ... (remaining 8472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 3618 21.73 - 43.47: 190 43.47 - 65.20: 28 65.20 - 86.93: 15 86.93 - 108.67: 4 Dihedral angle restraints: 3855 sinusoidal: 1652 harmonic: 2203 Sorted by residual: dihedral pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " pdb=" SG CYS H 305 " pdb=" CB CYS H 305 " ideal model delta sinusoidal sigma weight residual 93.00 42.18 50.82 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 303 " pdb=" CB CYS H 303 " ideal model delta sinusoidal sigma weight residual 93.00 137.73 -44.73 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CB CYS C 21 " pdb=" SG CYS C 21 " pdb=" SG CYS C 80 " pdb=" CB CYS C 80 " ideal model delta sinusoidal sigma weight residual 93.00 48.98 44.02 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 3852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 784 0.057 - 0.114: 124 0.114 - 0.171: 22 0.171 - 0.228: 0 0.228 - 0.285: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA CYS H 258 " pdb=" N CYS H 258 " pdb=" C CYS H 258 " pdb=" CB CYS H 258 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN H 33 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 929 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 121 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO H 122 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO H 122 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 122 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 97 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO H 98 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 264 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO H 265 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 265 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 265 " 0.022 5.00e-02 4.00e+02 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1375 2.79 - 3.32: 4910 3.32 - 3.85: 9912 3.85 - 4.37: 11986 4.37 - 4.90: 21051 Nonbonded interactions: 49234 Sorted by model distance: nonbonded pdb=" OH TYR D 33 " pdb=" OE1 GLU H 270 " model vdw 2.268 3.040 nonbonded pdb=" O VAL D 31 " pdb=" OG SER H 269 " model vdw 2.268 3.040 nonbonded pdb=" NH1 ARG C 30 " pdb=" OD1 ASP C 54 " model vdw 2.307 3.120 nonbonded pdb=" O GLU H 201 " pdb=" NH2 ARG H 241 " model vdw 2.311 3.120 nonbonded pdb=" NH1 ARG D 55 " pdb=" O PHE D 63 " model vdw 2.346 3.120 ... (remaining 49229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.003 0.083 6280 Z= 0.141 Angle : 0.635 14.058 8540 Z= 0.306 Chirality : 0.046 0.285 932 Planarity : 0.005 0.060 1088 Dihedral : 13.996 108.668 2422 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.20 (0.29), residues: 777 helix: 0.13 (0.63), residues: 70 sheet: 0.79 (0.33), residues: 232 loop : -0.65 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 322 TYR 0.009 0.001 TYR H 259 PHE 0.011 0.001 PHE H 130 TRP 0.010 0.001 TRP H 60 HIS 0.009 0.001 HIS H 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 6254) covalent geometry : angle 0.60226 / 0.29 ( 8477) SS BOND : bond 0.01070 / 0.69 ( 15) SS BOND : angle 2.45987 / 1.71 ( 30) hydrogen bonds : bond 0.21980 / 15.18 ( 215) hydrogen bonds : angle 8.15787 / 5.84 ( 582) link_ALPHA1-3 : bond 0.00166 / 0.08 ( 2) link_ALPHA1-3 : angle 2.05758 / 1.04 ( 6) link_ALPHA1-6 : bond 0.00516 / 0.27 ( 2) link_ALPHA1-6 : angle 1.65704 / 0.83 ( 6) link_BETA1-4 : bond 0.00587 / 0.29 ( 4) link_BETA1-4 : angle 2.82121 / 1.73 ( 12) link_NAG-ASN : bond 0.00462 / 0.22 ( 3) link_NAG-ASN : angle 2.30339 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.292 Fit side-chains REVERT: C 43 LYS cc_start: 0.8082 (mppt) cc_final: 0.7854 (mppt) REVERT: A 43 LYS cc_start: 0.7669 (mppt) cc_final: 0.7425 (mmtm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.7458 time to fit residues: 90.4309 Evaluate side-chains 106 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN H 68 GLN H 223 GLN ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103606 restraints weight = 6447.548| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.98 r_work: 0.3075 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 6280 Z= 0.213 Angle : 0.757 13.002 8540 Z= 0.390 Chirality : 0.051 0.274 932 Planarity : 0.006 0.062 1088 Dihedral : 9.029 78.457 1080 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.85 % Allowed : 8.95 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.47 (0.29), residues: 777 helix: -0.31 (0.58), residues: 76 sheet: 0.55 (0.30), residues: 277 loop : -0.90 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 43 TYR 0.014 0.002 TYR H 83 PHE 0.020 0.002 PHE H 130 TRP 0.012 0.002 TRP C 109 HIS 0.007 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 6254) covalent geometry : angle 0.72187 / 0.38 ( 8477) SS BOND : bond 0.01545 / 0.95 ( 15) SS BOND : angle 2.73959 / 2.02 ( 30) hydrogen bonds : bond 0.04649 / 3.30 ( 215) hydrogen bonds : angle 5.68999 / 4.12 ( 582) link_ALPHA1-3 : bond 0.00306 / 0.16 ( 2) link_ALPHA1-3 : angle 2.08471 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00304 / 0.16 ( 2) link_ALPHA1-6 : angle 1.56781 / 0.78 ( 6) link_BETA1-4 : bond 0.00601 / 0.30 ( 4) link_BETA1-4 : angle 3.25974 / 1.85 ( 12) link_NAG-ASN : bond 0.00321 / 0.16 ( 3) link_NAG-ASN : angle 2.98910 / 1.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.245 Fit side-chains REVERT: D 62 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7929 (ptm-80) REVERT: H 151 GLU cc_start: 0.7968 (tp30) cc_final: 0.7700 (tm-30) REVERT: H 246 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7962 (ttpp) REVERT: H 288 LYS cc_start: 0.7634 (ttmm) cc_final: 0.7072 (tttm) REVERT: A 43 LYS cc_start: 0.7987 (mppt) cc_final: 0.7629 (mmtm) REVERT: A 115 ARG cc_start: 0.8600 (ptt180) cc_final: 0.7877 (mmp80) REVERT: B 104 LYS cc_start: 0.8377 (tttp) cc_final: 0.7995 (tptt) outliers start: 12 outliers final: 5 residues processed: 117 average time/residue: 0.7310 time to fit residues: 88.6301 Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.107388 restraints weight = 6397.175| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.97 r_work: 0.3122 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6280 Z= 0.114 Angle : 0.610 9.506 8540 Z= 0.311 Chirality : 0.045 0.238 932 Planarity : 0.005 0.059 1088 Dihedral : 8.451 72.201 1080 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.70 % Allowed : 12.81 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.42 (0.29), residues: 777 helix: 0.10 (0.60), residues: 76 sheet: 0.58 (0.31), residues: 268 loop : -0.92 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 43 TYR 0.009 0.001 TYR H 83 PHE 0.016 0.001 PHE H 130 TRP 0.010 0.001 TRP H 141 HIS 0.003 0.001 HIS H 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 6254) covalent geometry : angle 0.57977 / 0.30 ( 8477) SS BOND : bond 0.00969 / 0.62 ( 15) SS BOND : angle 2.04014 / 1.48 ( 30) hydrogen bonds : bond 0.03513 / 2.49 ( 215) hydrogen bonds : angle 5.28783 / 3.79 ( 582) link_ALPHA1-3 : bond 0.00504 / 0.26 ( 2) link_ALPHA1-3 : angle 1.75629 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00506 / 0.26 ( 2) link_ALPHA1-6 : angle 1.44560 / 0.71 ( 6) link_BETA1-4 : bond 0.00538 / 0.27 ( 4) link_BETA1-4 : angle 3.05766 / 1.79 ( 12) link_NAG-ASN : bond 0.00490 / 0.24 ( 3) link_NAG-ASN : angle 2.66150 / 1.27 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.210 Fit side-chains REVERT: C 43 LYS cc_start: 0.8395 (mppt) cc_final: 0.8085 (mppt) REVERT: H 151 GLU cc_start: 0.7874 (tp30) cc_final: 0.7626 (tt0) REVERT: H 246 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7950 (ttpp) REVERT: A 43 LYS cc_start: 0.8050 (mppt) cc_final: 0.7692 (mptt) REVERT: A 115 ARG cc_start: 0.8518 (ptt180) cc_final: 0.7859 (mmp80) REVERT: B 104 LYS cc_start: 0.8330 (tttp) cc_final: 0.7957 (tptt) outliers start: 11 outliers final: 3 residues processed: 120 average time/residue: 0.7146 time to fit residues: 89.0266 Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain A residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103349 restraints weight = 6456.897| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.97 r_work: 0.3068 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 6280 Z= 0.203 Angle : 0.731 11.780 8540 Z= 0.372 Chirality : 0.050 0.275 932 Planarity : 0.006 0.061 1088 Dihedral : 8.847 75.557 1080 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.16 % Allowed : 13.12 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.48 (0.28), residues: 777 helix: 0.02 (0.60), residues: 76 sheet: 0.54 (0.30), residues: 278 loop : -0.98 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 43 TYR 0.014 0.002 TYR H 83 PHE 0.020 0.002 PHE H 130 TRP 0.012 0.002 TRP H 141 HIS 0.007 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 ( 6254) covalent geometry : angle 0.69326 / 0.36 ( 8477) SS BOND : bond 0.01550 / 0.96 ( 15) SS BOND : angle 2.71064 / 1.97 ( 30) hydrogen bonds : bond 0.04029 / 2.87 ( 215) hydrogen bonds : angle 5.22955 / 3.78 ( 582) link_ALPHA1-3 : bond 0.00338 / 0.18 ( 2) link_ALPHA1-3 : angle 1.89547 / 1.00 ( 6) link_ALPHA1-6 : bond 0.00396 / 0.20 ( 2) link_ALPHA1-6 : angle 1.46306 / 0.72 ( 6) link_BETA1-4 : bond 0.00527 / 0.26 ( 4) link_BETA1-4 : angle 3.41337 / 1.95 ( 12) link_NAG-ASN : bond 0.00268 / 0.13 ( 3) link_NAG-ASN : angle 3.23158 / 1.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.252 Fit side-chains REVERT: H 151 GLU cc_start: 0.7934 (tp30) cc_final: 0.7711 (tp30) REVERT: A 115 ARG cc_start: 0.8575 (ptt180) cc_final: 0.7894 (mmp80) REVERT: B 104 LYS cc_start: 0.8359 (tttp) cc_final: 0.7963 (tptt) outliers start: 14 outliers final: 9 residues processed: 114 average time/residue: 0.7310 time to fit residues: 86.5575 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.0670 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106189 restraints weight = 6475.572| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.98 r_work: 0.3107 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6280 Z= 0.122 Angle : 0.628 10.261 8540 Z= 0.316 Chirality : 0.046 0.248 932 Planarity : 0.005 0.059 1088 Dihedral : 8.366 70.105 1080 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.16 % Allowed : 13.73 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.44 (0.29), residues: 777 helix: 0.26 (0.62), residues: 76 sheet: 0.54 (0.31), residues: 271 loop : -0.96 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 43 TYR 0.010 0.001 TYR H 83 PHE 0.018 0.001 PHE H 130 TRP 0.012 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6254) covalent geometry : angle 0.59144 / 0.31 ( 8477) SS BOND : bond 0.01152 / 0.71 ( 15) SS BOND : angle 2.34330 / 1.63 ( 30) hydrogen bonds : bond 0.03213 / 2.28 ( 215) hydrogen bonds : angle 5.06392 / 3.63 ( 582) link_ALPHA1-3 : bond 0.00469 / 0.24 ( 2) link_ALPHA1-3 : angle 1.75524 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00455 / 0.23 ( 2) link_ALPHA1-6 : angle 1.47470 / 0.72 ( 6) link_BETA1-4 : bond 0.00547 / 0.27 ( 4) link_BETA1-4 : angle 3.18053 / 1.85 ( 12) link_NAG-ASN : bond 0.00466 / 0.22 ( 3) link_NAG-ASN : angle 2.98516 / 1.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.246 Fit side-chains REVERT: C 89 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: H 151 GLU cc_start: 0.7932 (tp30) cc_final: 0.7703 (tp30) REVERT: H 322 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7729 (mtp180) REVERT: A 43 LYS cc_start: 0.8066 (mptt) cc_final: 0.7605 (mmtm) REVERT: A 115 ARG cc_start: 0.8552 (ptt180) cc_final: 0.7880 (mmp80) REVERT: B 104 LYS cc_start: 0.8317 (tttp) cc_final: 0.7935 (tptt) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.7334 time to fit residues: 86.0043 Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 31 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108377 restraints weight = 6419.568| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.97 r_work: 0.3140 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 6280 Z= 0.103 Angle : 0.583 10.671 8540 Z= 0.291 Chirality : 0.045 0.217 932 Planarity : 0.005 0.058 1088 Dihedral : 7.895 64.212 1080 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.47 % Allowed : 14.81 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.28 (0.29), residues: 777 helix: 0.46 (0.63), residues: 76 sheet: 0.63 (0.31), residues: 271 loop : -0.85 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.009 0.001 TYR H 83 PHE 0.015 0.001 PHE H 130 TRP 0.011 0.001 TRP H 141 HIS 0.003 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 6254) covalent geometry : angle 0.54971 / 0.28 ( 8477) SS BOND : bond 0.00956 / 0.60 ( 15) SS BOND : angle 2.00574 / 1.41 ( 30) hydrogen bonds : bond 0.02868 / 2.03 ( 215) hydrogen bonds : angle 4.89479 / 3.51 ( 582) link_ALPHA1-3 : bond 0.00528 / 0.27 ( 2) link_ALPHA1-3 : angle 1.76129 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00473 / 0.24 ( 2) link_ALPHA1-6 : angle 1.47604 / 0.73 ( 6) link_BETA1-4 : bond 0.00512 / 0.26 ( 4) link_BETA1-4 : angle 3.08210 / 1.80 ( 12) link_NAG-ASN : bond 0.00426 / 0.20 ( 3) link_NAG-ASN : angle 2.93242 / 1.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.253 Fit side-chains REVERT: C 89 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: H 276 THR cc_start: 0.8539 (t) cc_final: 0.8332 (m) REVERT: H 288 LYS cc_start: 0.7585 (ttmp) cc_final: 0.7297 (ttmt) REVERT: A 43 LYS cc_start: 0.7997 (mptt) cc_final: 0.7499 (mmtm) REVERT: A 115 ARG cc_start: 0.8510 (ptt180) cc_final: 0.7857 (mmp80) REVERT: B 104 LYS cc_start: 0.8299 (tttp) cc_final: 0.7927 (tptt) outliers start: 16 outliers final: 4 residues processed: 117 average time/residue: 0.7269 time to fit residues: 88.2339 Evaluate side-chains 110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105561 restraints weight = 6439.548| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.98 r_work: 0.3101 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 6280 Z= 0.147 Angle : 0.667 11.842 8540 Z= 0.335 Chirality : 0.047 0.243 932 Planarity : 0.005 0.058 1088 Dihedral : 8.150 66.531 1080 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.54 % Allowed : 15.74 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.36 (0.29), residues: 777 helix: 0.34 (0.62), residues: 76 sheet: 0.59 (0.31), residues: 271 loop : -0.90 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 43 TYR 0.012 0.001 TYR H 83 PHE 0.017 0.002 PHE H 130 TRP 0.012 0.002 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 ( 6254) covalent geometry : angle 0.62649 / 0.32 ( 8477) SS BOND : bond 0.01449 / 0.86 ( 15) SS BOND : angle 2.65537 / 1.83 ( 30) hydrogen bonds : bond 0.03296 / 2.34 ( 215) hydrogen bonds : angle 4.94917 / 3.58 ( 582) link_ALPHA1-3 : bond 0.00423 / 0.22 ( 2) link_ALPHA1-3 : angle 1.82427 / 0.96 ( 6) link_ALPHA1-6 : bond 0.00391 / 0.20 ( 2) link_ALPHA1-6 : angle 1.52537 / 0.76 ( 6) link_BETA1-4 : bond 0.00529 / 0.26 ( 4) link_BETA1-4 : angle 3.18387 / 1.83 ( 12) link_NAG-ASN : bond 0.00336 / 0.16 ( 3) link_NAG-ASN : angle 3.49293 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: C 89 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: H 151 GLU cc_start: 0.7803 (tp30) cc_final: 0.7542 (tm-30) REVERT: A 43 LYS cc_start: 0.8042 (mptt) cc_final: 0.7507 (mmtm) REVERT: A 115 ARG cc_start: 0.8549 (ptt180) cc_final: 0.7878 (mmp80) REVERT: B 104 LYS cc_start: 0.8358 (tttp) cc_final: 0.7965 (tptt) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.7529 time to fit residues: 85.1408 Evaluate side-chains 109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107406 restraints weight = 6396.782| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.97 r_work: 0.3120 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 6280 Z= 0.118 Angle : 0.618 10.926 8540 Z= 0.309 Chirality : 0.046 0.232 932 Planarity : 0.005 0.058 1088 Dihedral : 7.913 63.885 1080 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.39 % Allowed : 16.51 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.30 (0.29), residues: 777 helix: 0.43 (0.62), residues: 76 sheet: 0.63 (0.31), residues: 271 loop : -0.88 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.010 0.001 TYR H 83 PHE 0.016 0.001 PHE H 130 TRP 0.011 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.11 ( 6254) covalent geometry : angle 0.58050 / 0.30 ( 8477) SS BOND : bond 0.01131 / 0.70 ( 15) SS BOND : angle 2.39212 / 1.64 ( 30) hydrogen bonds : bond 0.02984 / 2.11 ( 215) hydrogen bonds : angle 4.92880 / 3.55 ( 582) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 2) link_ALPHA1-3 : angle 1.75908 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00428 / 0.22 ( 2) link_ALPHA1-6 : angle 1.49564 / 0.74 ( 6) link_BETA1-4 : bond 0.00535 / 0.27 ( 4) link_BETA1-4 : angle 3.06635 / 1.79 ( 12) link_NAG-ASN : bond 0.00414 / 0.20 ( 3) link_NAG-ASN : angle 3.06617 / 1.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.250 Fit side-chains REVERT: C 89 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: H 151 GLU cc_start: 0.7741 (tp30) cc_final: 0.7481 (tm-30) REVERT: H 276 THR cc_start: 0.8540 (t) cc_final: 0.8323 (m) REVERT: A 43 LYS cc_start: 0.7981 (mptt) cc_final: 0.7534 (mmtm) REVERT: A 115 ARG cc_start: 0.8513 (ptt180) cc_final: 0.7859 (mmp80) REVERT: B 104 LYS cc_start: 0.8300 (tttp) cc_final: 0.7929 (tptt) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.7467 time to fit residues: 85.2001 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106573 restraints weight = 6447.045| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.98 r_work: 0.3116 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 6280 Z= 0.124 Angle : 0.633 10.979 8540 Z= 0.316 Chirality : 0.046 0.232 932 Planarity : 0.005 0.058 1088 Dihedral : 7.899 63.272 1080 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.39 % Allowed : 16.51 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.31 (0.29), residues: 777 helix: 0.43 (0.62), residues: 76 sheet: 0.64 (0.31), residues: 271 loop : -0.90 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.011 0.001 TYR H 83 PHE 0.016 0.001 PHE H 130 TRP 0.011 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 6254) covalent geometry : angle 0.59362 / 0.30 ( 8477) SS BOND : bond 0.01151 / 0.71 ( 15) SS BOND : angle 2.36628 / 1.64 ( 30) hydrogen bonds : bond 0.03032 / 2.14 ( 215) hydrogen bonds : angle 4.91481 / 3.55 ( 582) link_ALPHA1-3 : bond 0.00491 / 0.26 ( 2) link_ALPHA1-3 : angle 1.77592 / 0.93 ( 6) link_ALPHA1-6 : bond 0.00414 / 0.21 ( 2) link_ALPHA1-6 : angle 1.50552 / 0.75 ( 6) link_BETA1-4 : bond 0.00523 / 0.26 ( 4) link_BETA1-4 : angle 3.10812 / 1.80 ( 12) link_NAG-ASN : bond 0.00383 / 0.18 ( 3) link_NAG-ASN : angle 3.70560 / 1.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 89 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: H 276 THR cc_start: 0.8547 (t) cc_final: 0.8331 (m) REVERT: A 43 LYS cc_start: 0.7989 (mptt) cc_final: 0.7546 (mmtm) REVERT: A 115 ARG cc_start: 0.8519 (ptt180) cc_final: 0.7876 (mmp80) REVERT: B 104 LYS cc_start: 0.8293 (tttp) cc_final: 0.7909 (tptt) outliers start: 9 outliers final: 7 residues processed: 109 average time/residue: 0.7667 time to fit residues: 86.5799 Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.103582 restraints weight = 6481.188| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.97 r_work: 0.3073 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 6280 Z= 0.198 Angle : 0.730 12.743 8540 Z= 0.368 Chirality : 0.050 0.272 932 Planarity : 0.006 0.058 1088 Dihedral : 8.470 69.296 1080 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.85 % Allowed : 16.36 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.45 (0.29), residues: 777 helix: 0.18 (0.60), residues: 76 sheet: 0.58 (0.31), residues: 268 loop : -0.97 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 43 TYR 0.014 0.002 TYR H 83 PHE 0.020 0.002 PHE H 130 TRP 0.012 0.002 TRP H 141 HIS 0.007 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.19 ( 6254) covalent geometry : angle 0.68742 / 0.36 ( 8477) SS BOND : bond 0.01479 / 0.91 ( 15) SS BOND : angle 2.74894 / 1.97 ( 30) hydrogen bonds : bond 0.03696 / 2.62 ( 215) hydrogen bonds : angle 5.07256 / 3.68 ( 582) link_ALPHA1-3 : bond 0.00378 / 0.20 ( 2) link_ALPHA1-3 : angle 1.75955 / 0.93 ( 6) link_ALPHA1-6 : bond 0.00359 / 0.18 ( 2) link_ALPHA1-6 : angle 1.47993 / 0.74 ( 6) link_BETA1-4 : bond 0.00527 / 0.26 ( 4) link_BETA1-4 : angle 3.40853 / 1.93 ( 12) link_NAG-ASN : bond 0.00320 / 0.15 ( 3) link_NAG-ASN : angle 3.98068 / 1.86 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.256 Fit side-chains REVERT: C 89 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: H 151 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: A 43 LYS cc_start: 0.8036 (mptt) cc_final: 0.7560 (mmtm) REVERT: A 115 ARG cc_start: 0.8534 (ptt180) cc_final: 0.7895 (mmp80) REVERT: B 104 LYS cc_start: 0.8372 (tttp) cc_final: 0.7972 (tptt) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.7753 time to fit residues: 85.0948 Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 21 optimal weight: 0.0070 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104838 restraints weight = 6441.244| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.97 r_work: 0.3091 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 6280 Z= 0.147 Angle : 0.673 11.686 8540 Z= 0.338 Chirality : 0.048 0.260 932 Planarity : 0.005 0.058 1088 Dihedral : 8.251 67.180 1080 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.23 % Allowed : 16.98 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.40 (0.29), residues: 777 helix: 0.28 (0.61), residues: 76 sheet: 0.66 (0.31), residues: 263 loop : -0.96 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 43 TYR 0.012 0.001 TYR H 83 PHE 0.018 0.002 PHE H 130 TRP 0.012 0.002 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 6254) covalent geometry : angle 0.63280 / 0.33 ( 8477) SS BOND : bond 0.01258 / 0.77 ( 15) SS BOND : angle 2.49338 / 1.76 ( 30) hydrogen bonds : bond 0.03320 / 2.35 ( 215) hydrogen bonds : angle 5.02777 / 3.63 ( 582) link_ALPHA1-3 : bond 0.00449 / 0.23 ( 2) link_ALPHA1-3 : angle 1.74392 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00404 / 0.20 ( 2) link_ALPHA1-6 : angle 1.49267 / 0.74 ( 6) link_BETA1-4 : bond 0.00544 / 0.27 ( 4) link_BETA1-4 : angle 3.28970 / 1.89 ( 12) link_NAG-ASN : bond 0.00396 / 0.19 ( 3) link_NAG-ASN : angle 3.66374 / 1.70 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.41 seconds wall clock time: 49 minutes 25.41 seconds (2965.41 seconds total)