Starting phenix.real_space_refine on Wed Mar 4 12:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk7_25175/03_2026/7sk7_25175_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk7_25175/03_2026/7sk7_25175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sk7_25175/03_2026/7sk7_25175_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk7_25175/03_2026/7sk7_25175_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sk7_25175/03_2026/7sk7_25175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk7_25175/03_2026/7sk7_25175.map" } resolution = 3.3 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= 0.062 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 39 5.16 5 C 4415 2.51 5 N 1114 2.21 5 O 1237 1.98 5 H 6650 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13455 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 4398 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 267, 4398 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 3 bond proxies already assigned to first conformer: 4444 Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1050 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "C" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3211 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "D" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3179 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain breaks: 2 Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1537 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 4 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'CLR': 1, 'GJ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS A 121 " occ=0.50 ... (29 atoms not shown) pdb=" HE1BHIS A 121 " occ=0.50 Time building chain proxies: 3.48, per 1000 atoms: 0.26 Number of scatterers: 13455 At special positions: 0 Unit cell: (83.16, 88.56, 142.56, 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 39 16.00 O 1237 8.00 N 1114 7.00 C 4415 6.00 H 6650 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " 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 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 625.8 milliseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 14 sheets defined 30.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 38 through 71 removed outlier: 4.472A pdb=" N VAL A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.833A pdb=" N THR A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.787A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.502A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 182 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.057A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 317 removed outlier: 4.665A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.190A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 removed outlier: 3.618A pdb=" N LYS C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 215 through 219 Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.506A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 33 removed outlier: 4.559A pdb=" N VAL A 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 25 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 187 removed outlier: 4.009A pdb=" N ARG A 197 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.535A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.744A pdb=" N VAL C 134 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN C 139 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 155 through 156 removed outlier: 4.746A pdb=" N TRP C 149 " --> pdb=" O GLN C 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.960A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 82 " --> pdb=" O CYS D 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.583A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR D 117 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.583A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 95 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 97 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.560A pdb=" N LYS D 158 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 135 through 139 removed outlier: 3.560A pdb=" N LYS D 158 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.696A pdb=" N THR D 166 " --> pdb=" O ASN D 214 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR D 209 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 6 through 7 removed outlier: 3.534A pdb=" N CYS K 22 " --> pdb=" O VAL K 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.764A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE K 98 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 947 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: 3.00 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6639 1.03 - 1.23: 42 1.23 - 1.42: 2993 1.42 - 1.62: 3912 1.62 - 1.82: 51 Bond restraints: 13637 Sorted by residual: bond pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.446 1.521 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C14 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.416 1.473 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C20 CLR A 402 " pdb=" C22 CLR A 402 " ideal model delta sigma weight residual 1.535 1.592 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.495 1.550 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C14 CLR A 402 " pdb=" C15 CLR A 402 " ideal model delta sigma weight residual 1.523 1.578 -0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 13632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 24284 1.70 - 3.40: 185 3.40 - 5.11: 31 5.11 - 6.81: 10 6.81 - 8.51: 3 Bond angle restraints: 24513 Sorted by residual: angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 103.44 8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" C08 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 108.48 116.45 -7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" C04 GJ9 A 401 " pdb=" N05 GJ9 A 401 " pdb=" C06 GJ9 A 401 " ideal model delta sigma weight residual 118.70 111.43 7.27 3.00e+00 1.11e-01 5.87e+00 angle pdb=" CA PRO C 41 " pdb=" N PRO C 41 " pdb=" CD PRO C 41 " ideal model delta sigma weight residual 112.00 108.80 3.20 1.40e+00 5.10e-01 5.22e+00 angle pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " pdb=" C25 CLR A 402 " ideal model delta sigma weight residual 115.14 108.51 6.63 3.00e+00 1.11e-01 4.88e+00 ... (remaining 24508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5977 17.70 - 35.41: 487 35.41 - 53.11: 122 53.11 - 70.82: 17 70.82 - 88.52: 10 Dihedral angle restraints: 6613 sinusoidal: 3512 harmonic: 3101 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -124.77 38.77 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CB CYS B 9 " pdb=" SG CYS B 9 " pdb=" SG CYS B 34 " pdb=" CB CYS B 34 " ideal model delta sinusoidal sigma weight residual -86.00 -59.31 -26.69 1 1.00e+01 1.00e-02 1.02e+01 dihedral pdb=" CA SER C 51 " pdb=" C SER C 51 " pdb=" N ALA C 52 " pdb=" CA ALA C 52 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 991 0.079 - 0.157: 83 0.157 - 0.236: 2 0.236 - 0.314: 1 0.314 - 0.393: 2 Chirality restraints: 1079 Sorted by residual: chirality pdb=" N10 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C34 GJ9 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.62 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C13 CLR A 402 " pdb=" C12 CLR A 402 " pdb=" C14 CLR A 402 " pdb=" C17 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.93 -3.32 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C20 CLR A 402 " pdb=" C17 CLR A 402 " pdb=" C21 CLR A 402 " pdb=" C22 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.59 2.83 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1076 not shown) Planarity restraints: 1968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 41 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 59 " -0.036 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO C 60 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 97 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A 98 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.027 5.00e-02 4.00e+02 ... (remaining 1965 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1077 2.22 - 2.81: 27945 2.81 - 3.41: 34015 3.41 - 4.00: 47255 4.00 - 4.60: 71520 Nonbonded interactions: 181812 Sorted by model distance: nonbonded pdb=" H VAL C 34 " pdb=" O SER C 51 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLN C 101 " pdb=" H GLN C 101 " model vdw 1.687 2.450 nonbonded pdb=" O ASP C 83 " pdb=" HH TYR C 87 " model vdw 1.698 2.450 nonbonded pdb=" OD1 ASN K 84 " pdb=" H SER K 85 " model vdw 1.702 2.450 nonbonded pdb=" O HIS C 190 " pdb=" HE ARG C 212 " model vdw 1.723 2.450 ... (remaining 181807 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.630 Find NCS groups from input model: 0.060 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6995 Z= 0.200 Angle : 0.572 8.509 9534 Z= 0.273 Chirality : 0.045 0.393 1079 Planarity : 0.004 0.083 1167 Dihedral : 14.161 88.521 2527 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.04 (0.30), residues: 827 helix: 1.11 (0.35), residues: 228 sheet: -0.02 (0.34), residues: 255 loop : -0.71 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.015 0.001 TYR D 53 PHE 0.009 0.001 PHE B 14 TRP 0.009 0.001 TRP A 208 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 6987) covalent geometry : angle 0.57123 ( 9518) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.88215 ( 16) hydrogen bonds : bond 0.22033 ( 317) hydrogen bonds : angle 8.46130 ( 947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2018 time to fit residues: 36.3488 Evaluate side-chains 118 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS C 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114519 restraints weight = 29131.549| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.22 r_work: 0.3270 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6995 Z= 0.201 Angle : 0.575 5.058 9534 Z= 0.307 Chirality : 0.043 0.142 1079 Planarity : 0.005 0.052 1167 Dihedral : 6.101 57.658 1034 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.06 % Allowed : 6.10 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.18 (0.29), residues: 827 helix: 1.11 (0.34), residues: 234 sheet: -0.07 (0.32), residues: 265 loop : -0.98 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 25 TYR 0.020 0.002 TYR D 53 PHE 0.011 0.001 PHE A 294 TRP 0.009 0.002 TRP A 208 HIS 0.006 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 6987) covalent geometry : angle 0.57390 ( 9518) SS BOND : bond 0.00460 ( 8) SS BOND : angle 1.00177 ( 16) hydrogen bonds : bond 0.05776 ( 317) hydrogen bonds : angle 5.73359 ( 947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ASP cc_start: 0.7470 (m-30) cc_final: 0.7244 (m-30) outliers start: 8 outliers final: 7 residues processed: 124 average time/residue: 0.2081 time to fit residues: 33.7097 Evaluate side-chains 121 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN K 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116120 restraints weight = 28193.781| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.19 r_work: 0.3272 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6995 Z= 0.135 Angle : 0.518 4.946 9534 Z= 0.272 Chirality : 0.041 0.141 1079 Planarity : 0.004 0.047 1167 Dihedral : 5.790 56.457 1034 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.53 % Allowed : 8.62 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.06 (0.30), residues: 827 helix: 1.38 (0.34), residues: 236 sheet: -0.04 (0.32), residues: 267 loop : -1.05 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 67 TYR 0.017 0.001 TYR D 53 PHE 0.010 0.001 PHE A 294 TRP 0.008 0.001 TRP A 208 HIS 0.004 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6987) covalent geometry : angle 0.51767 ( 9518) SS BOND : bond 0.00354 ( 8) SS BOND : angle 0.69170 ( 16) hydrogen bonds : bond 0.04702 ( 317) hydrogen bonds : angle 5.21401 ( 947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7120 (mm-30) outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.1923 time to fit residues: 31.9123 Evaluate side-chains 115 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN K 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115873 restraints weight = 30712.015| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.30 r_work: 0.3247 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6995 Z= 0.127 Angle : 0.504 4.791 9534 Z= 0.263 Chirality : 0.041 0.133 1079 Planarity : 0.004 0.046 1167 Dihedral : 5.697 54.728 1034 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 9.28 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.06 (0.29), residues: 827 helix: 1.52 (0.34), residues: 235 sheet: 0.10 (0.32), residues: 263 loop : -1.06 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.014 0.001 TYR D 53 PHE 0.011 0.001 PHE A 233 TRP 0.007 0.001 TRP A 208 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6987) covalent geometry : angle 0.50343 ( 9518) SS BOND : bond 0.00332 ( 8) SS BOND : angle 0.70229 ( 16) hydrogen bonds : bond 0.04220 ( 317) hydrogen bonds : angle 4.95934 ( 947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7140 (mm-30) outliers start: 7 outliers final: 6 residues processed: 122 average time/residue: 0.1822 time to fit residues: 29.8667 Evaluate side-chains 116 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain K residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN K 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115311 restraints weight = 30933.202| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.31 r_work: 0.3242 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6995 Z= 0.142 Angle : 0.515 4.889 9534 Z= 0.267 Chirality : 0.041 0.134 1079 Planarity : 0.004 0.046 1167 Dihedral : 5.719 55.320 1034 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.66 % Allowed : 10.88 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.03 (0.29), residues: 827 helix: 1.53 (0.34), residues: 235 sheet: 0.07 (0.32), residues: 269 loop : -1.12 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 53 TYR 0.014 0.001 TYR D 53 PHE 0.012 0.001 PHE A 233 TRP 0.006 0.001 TRP A 208 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6987) covalent geometry : angle 0.51498 ( 9518) SS BOND : bond 0.00352 ( 8) SS BOND : angle 0.75161 ( 16) hydrogen bonds : bond 0.04194 ( 317) hydrogen bonds : angle 4.89120 ( 947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7154 (mm-30) outliers start: 5 outliers final: 5 residues processed: 119 average time/residue: 0.1938 time to fit residues: 30.7660 Evaluate side-chains 117 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain K residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115640 restraints weight = 28206.489| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.19 r_work: 0.3270 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6995 Z= 0.146 Angle : 0.514 4.882 9534 Z= 0.267 Chirality : 0.041 0.134 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.751 56.427 1034 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.19 % Allowed : 11.27 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.03 (0.30), residues: 827 helix: 1.55 (0.34), residues: 235 sheet: 0.01 (0.32), residues: 267 loop : -1.06 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 25 TYR 0.013 0.001 TYR D 53 PHE 0.012 0.001 PHE A 233 TRP 0.006 0.001 TRP A 208 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6987) covalent geometry : angle 0.51360 ( 9518) SS BOND : bond 0.00370 ( 8) SS BOND : angle 0.76630 ( 16) hydrogen bonds : bond 0.04146 ( 317) hydrogen bonds : angle 4.82427 ( 947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 TYR cc_start: 0.9185 (p90) cc_final: 0.8968 (p90) outliers start: 9 outliers final: 9 residues processed: 121 average time/residue: 0.1910 time to fit residues: 31.1293 Evaluate side-chains 124 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117152 restraints weight = 34059.947| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.42 r_work: 0.3250 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6995 Z= 0.127 Angle : 0.503 4.759 9534 Z= 0.260 Chirality : 0.041 0.133 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.700 56.501 1034 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.06 % Allowed : 12.07 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.13 (0.30), residues: 827 helix: 1.66 (0.35), residues: 235 sheet: 0.03 (0.32), residues: 267 loop : -0.99 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 25 TYR 0.012 0.001 TYR D 58 PHE 0.009 0.001 PHE A 294 TRP 0.006 0.001 TRP A 265 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6987) covalent geometry : angle 0.50246 ( 9518) SS BOND : bond 0.00326 ( 8) SS BOND : angle 0.70196 ( 16) hydrogen bonds : bond 0.03959 ( 317) hydrogen bonds : angle 4.73971 ( 947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7184 (mm-30) REVERT: C 161 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7465 (mt0) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.1819 time to fit residues: 29.6170 Evaluate side-chains 122 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114526 restraints weight = 29936.716| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.27 r_work: 0.3240 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6995 Z= 0.148 Angle : 0.515 4.856 9534 Z= 0.267 Chirality : 0.041 0.133 1079 Planarity : 0.004 0.044 1167 Dihedral : 5.757 57.555 1034 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.72 % Allowed : 11.67 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.12 (0.30), residues: 827 helix: 1.64 (0.34), residues: 235 sheet: 0.10 (0.32), residues: 260 loop : -1.03 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 25 TYR 0.013 0.001 TYR C 87 PHE 0.010 0.001 PHE A 294 TRP 0.006 0.001 TRP D 50 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6987) covalent geometry : angle 0.51420 ( 9518) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.76172 ( 16) hydrogen bonds : bond 0.04048 ( 317) hydrogen bonds : angle 4.74298 ( 947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 161 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7440 (mt0) outliers start: 13 outliers final: 12 residues processed: 127 average time/residue: 0.1865 time to fit residues: 31.9239 Evaluate side-chains 128 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 42 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118062 restraints weight = 30570.009| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.29 r_work: 0.3309 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6995 Z= 0.105 Angle : 0.489 4.592 9534 Z= 0.252 Chirality : 0.041 0.149 1079 Planarity : 0.004 0.046 1167 Dihedral : 5.589 57.888 1034 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.33 % Allowed : 12.20 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 (0.30), residues: 827 helix: 1.84 (0.35), residues: 235 sheet: 0.19 (0.32), residues: 260 loop : -0.95 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 109 TYR 0.011 0.001 TYR D 60 PHE 0.008 0.001 PHE A 294 TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6987) covalent geometry : angle 0.48883 ( 9518) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.57277 ( 16) hydrogen bonds : bond 0.03685 ( 317) hydrogen bonds : angle 4.59106 ( 947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7091 (mm-30) REVERT: C 161 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7450 (mt0) outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 0.1899 time to fit residues: 31.4370 Evaluate side-chains 125 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116869 restraints weight = 31391.689| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.44 r_work: 0.3293 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6995 Z= 0.115 Angle : 0.496 4.640 9534 Z= 0.256 Chirality : 0.041 0.141 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.577 57.227 1034 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.46 % Allowed : 12.20 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.37 (0.30), residues: 827 helix: 1.84 (0.34), residues: 235 sheet: 0.27 (0.32), residues: 260 loop : -0.92 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 19 TYR 0.011 0.001 TYR D 60 PHE 0.009 0.001 PHE A 294 TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6987) covalent geometry : angle 0.49575 ( 9518) SS BOND : bond 0.00295 ( 8) SS BOND : angle 0.62849 ( 16) hydrogen bonds : bond 0.03698 ( 317) hydrogen bonds : angle 4.56665 ( 947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7046 (mm-30) REVERT: C 161 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7476 (mt0) outliers start: 11 outliers final: 10 residues processed: 129 average time/residue: 0.1905 time to fit residues: 32.6150 Evaluate side-chains 128 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117770 restraints weight = 27901.409| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.28 r_work: 0.3304 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6995 Z= 0.120 Angle : 0.502 4.682 9534 Z= 0.259 Chirality : 0.041 0.138 1079 Planarity : 0.004 0.045 1167 Dihedral : 5.577 57.861 1034 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.59 % Allowed : 12.47 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 (0.30), residues: 827 helix: 1.86 (0.34), residues: 235 sheet: 0.30 (0.32), residues: 260 loop : -0.91 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.015 0.001 TYR D 60 PHE 0.009 0.001 PHE A 294 TRP 0.008 0.001 TRP D 50 HIS 0.003 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6987) covalent geometry : angle 0.50218 ( 9518) SS BOND : bond 0.00287 ( 8) SS BOND : angle 0.64270 ( 16) hydrogen bonds : bond 0.03702 ( 317) hydrogen bonds : angle 4.55017 ( 947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.55 seconds wall clock time: 71 minutes 30.29 seconds (4290.29 seconds total)