Starting phenix.real_space_refine on Wed Jan 15 19:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zz0_60585/01_2025/8zz0_60585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zz0_60585/01_2025/8zz0_60585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zz0_60585/01_2025/8zz0_60585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zz0_60585/01_2025/8zz0_60585.map" model { file = "/net/cci-nas-00/data/ceres_data/8zz0_60585/01_2025/8zz0_60585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zz0_60585/01_2025/8zz0_60585.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 78 5.16 5 C 5745 2.51 5 N 1471 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 361 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 368 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "C" Number of atoms: 1606 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1616 Chain: "D" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1621 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH G 301 " occ=0.68 Time building chain proxies: 5.88, per 1000 atoms: 0.66 Number of scatterers: 8914 At special positions: 0 Unit cell: (102.6, 98.55, 105.3, 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 78 16.00 O 1620 8.00 N 1471 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 1 sheets defined 91.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.908A pdb=" N GLY A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.005A pdb=" N PHE B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.528A pdb=" N ILE C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 68 Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.602A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 168 removed outlier: 3.543A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.928A pdb=" N MET C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 228 Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.540A pdb=" N ILE C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 removed outlier: 3.605A pdb=" N GLU C 244 " --> pdb=" O TYR C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.792A pdb=" N MET D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.744A pdb=" N ASP D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 87 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 117 through 168 Proline residue: D 151 - end of helix removed outlier: 3.666A pdb=" N ASN D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 195 removed outlier: 4.306A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 Processing helix chain 'D' and resid 232 through 239 removed outlier: 3.657A pdb=" N SER D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.841A pdb=" N ARG D 247 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 48 removed outlier: 3.661A pdb=" N ASP E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 72 through 87 removed outlier: 3.827A pdb=" N LEU E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 117 through 168 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 171 through 196 removed outlier: 3.852A pdb=" N GLY E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Proline residue: E 177 - end of helix removed outlier: 3.599A pdb=" N VAL E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 228 Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.695A pdb=" N TYR E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 removed outlier: 6.739A pdb=" N GLY E 245 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS E 246 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 247 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 248' Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 51 through 68 Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.681A pdb=" N GLY F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 168 Proline residue: F 151 - end of helix Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 195 removed outlier: 3.634A pdb=" N THR F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 228 Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 244 through 251 removed outlier: 4.113A pdb=" N ARG F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 249 " --> pdb=" O LYS F 246 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 50 Processing helix chain 'G' and resid 51 through 67 Processing helix chain 'G' and resid 72 through 87 removed outlier: 3.769A pdb=" N LEU G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 115 Processing helix chain 'G' and resid 117 through 169 removed outlier: 3.829A pdb=" N VAL G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 171 through 195 removed outlier: 3.529A pdb=" N GLY G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) Proline residue: G 177 - end of helix Processing helix chain 'G' and resid 196 through 228 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.521A pdb=" N LYS G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.934A pdb=" N ARG G 247 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 808 hydrogen bonds defined for protein. 2399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2896 1.35 - 1.47: 1892 1.47 - 1.58: 4093 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 9035 Sorted by residual: bond pdb=" CB PRO G 172 " pdb=" CG PRO G 172 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 bond pdb=" CB ASP F 227 " pdb=" CG ASP F 227 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.19e+00 bond pdb=" CA ASP C 171 " pdb=" CB ASP C 171 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.38e-02 5.25e+03 2.15e+00 bond pdb=" CA ASP F 170 " pdb=" CB ASP F 170 " ideal model delta sigma weight residual 1.534 1.557 -0.023 1.55e-02 4.16e+03 2.15e+00 bond pdb=" CA ASP F 227 " pdb=" CB ASP F 227 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.68e-02 3.54e+03 1.89e+00 ... (remaining 9030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 12014 2.00 - 4.00: 116 4.00 - 6.00: 32 6.00 - 8.01: 6 8.01 - 10.01: 1 Bond angle restraints: 12169 Sorted by residual: angle pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " pdb=" CD LYS B 48 " ideal model delta sigma weight residual 111.30 118.38 -7.08 2.30e+00 1.89e-01 9.48e+00 angle pdb=" CA PRO E 172 " pdb=" N PRO E 172 " pdb=" CD PRO E 172 " ideal model delta sigma weight residual 112.00 107.80 4.20 1.40e+00 5.10e-01 9.00e+00 angle pdb=" CA LEU F 112 " pdb=" CB LEU F 112 " pdb=" CG LEU F 112 " ideal model delta sigma weight residual 116.30 126.31 -10.01 3.50e+00 8.16e-02 8.18e+00 angle pdb=" CA ASP F 227 " pdb=" CB ASP F 227 " pdb=" CG ASP F 227 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.00e+00 1.00e+00 8.16e+00 angle pdb=" CG ARG E 216 " pdb=" CD ARG E 216 " pdb=" NE ARG E 216 " ideal model delta sigma weight residual 112.00 117.90 -5.90 2.20e+00 2.07e-01 7.20e+00 ... (remaining 12164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 4617 18.18 - 36.35: 627 36.35 - 54.53: 179 54.53 - 72.70: 20 72.70 - 90.88: 7 Dihedral angle restraints: 5450 sinusoidal: 2132 harmonic: 3318 Sorted by residual: dihedral pdb=" CB GLU D 72 " pdb=" CG GLU D 72 " pdb=" CD GLU D 72 " pdb=" OE1 GLU D 72 " ideal model delta sinusoidal sigma weight residual 0.00 90.88 -90.88 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" CA ASN G 243 " pdb=" CB ASN G 243 " pdb=" CG ASN G 243 " pdb=" OD1 ASN G 243 " ideal model delta sinusoidal sigma weight residual 120.00 -169.82 -70.18 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP E 85 " pdb=" CB ASP E 85 " pdb=" CG ASP E 85 " pdb=" OD1 ASP E 85 " ideal model delta sinusoidal sigma weight residual -30.00 -84.40 54.40 1 2.00e+01 2.50e-03 1.00e+01 ... (remaining 5447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1193 0.050 - 0.099: 226 0.099 - 0.148: 27 0.148 - 0.198: 0 0.198 - 0.247: 1 Chirality restraints: 1447 Sorted by residual: chirality pdb=" CB VAL D 39 " pdb=" CA VAL D 39 " pdb=" CG1 VAL D 39 " pdb=" CG2 VAL D 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU F 112 " pdb=" CB LEU F 112 " pdb=" CD1 LEU F 112 " pdb=" CD2 LEU F 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA PRO G 73 " pdb=" N PRO G 73 " pdb=" C PRO G 73 " pdb=" CB PRO G 73 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1444 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 171 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO E 172 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 171 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.49e+01 pdb=" N PRO G 172 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO G 172 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 172 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 227 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ASP F 227 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP F 227 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY F 228 " -0.013 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 84 2.68 - 3.23: 8961 3.23 - 3.79: 14453 3.79 - 4.34: 17960 4.34 - 4.90: 30596 Nonbonded interactions: 72054 Sorted by model distance: nonbonded pdb=" OG1 THR E 158 " pdb=" OG1 THR E 186 " model vdw 2.123 3.040 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.169 3.040 nonbonded pdb=" O LEU B 45 " pdb=" NE2 GLN B 49 " model vdw 2.181 3.120 nonbonded pdb=" N GLU E 72 " pdb=" OE1 GLU E 72 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU C 74 " pdb=" NH2 ARG C 247 " model vdw 2.276 3.120 ... (remaining 72049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 59) } ncs_group { reference = (chain 'C' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'D' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'E' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'F' and (resid 15 through 16 or resid 31 through 154 or resid 156 through \ 250)) selection = (chain 'G' and (resid 29 through 154 or resid 156 through 250)) } 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.540 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 0.076 9035 Z= 0.193 Angle : 0.582 10.008 12169 Z= 0.309 Chirality : 0.037 0.247 1447 Planarity : 0.005 0.100 1544 Dihedral : 17.581 90.879 3310 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 25.82 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.25), residues: 1149 helix: 2.36 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -0.67 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.008 0.001 HIS E 116 PHE 0.018 0.001 PHE G 44 TYR 0.016 0.001 TYR E 237 ARG 0.009 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: E 169 MET cc_start: 0.8074 (tpp) cc_final: 0.7377 (ttm) REVERT: F 20 MET cc_start: 0.2868 (ptm) cc_final: 0.1922 (tpt) REVERT: F 105 MET cc_start: 0.8202 (tpt) cc_final: 0.7676 (ttp) REVERT: F 173 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7276 (tttm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2385 time to fit residues: 57.2046 Evaluate side-chains 172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 243 ASN E 168 ASN E 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.189915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153137 restraints weight = 11576.936| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.94 r_work: 0.3042 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9035 Z= 0.170 Angle : 0.492 7.118 12169 Z= 0.255 Chirality : 0.037 0.169 1447 Planarity : 0.004 0.067 1544 Dihedral : 3.451 13.739 1223 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.70 % Allowed : 23.59 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.25), residues: 1149 helix: 2.63 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.61 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.005 0.001 HIS E 116 PHE 0.016 0.001 PHE G 44 TYR 0.009 0.001 TYR E 237 ARG 0.005 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: C 219 MET cc_start: 0.6395 (ttp) cc_final: 0.5868 (ttt) REVERT: E 169 MET cc_start: 0.8257 (tpp) cc_final: 0.7906 (ttm) REVERT: F 20 MET cc_start: 0.2404 (ptm) cc_final: 0.1415 (tpt) REVERT: F 105 MET cc_start: 0.8113 (tpt) cc_final: 0.7557 (ttp) REVERT: F 173 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7094 (tttm) outliers start: 16 outliers final: 10 residues processed: 194 average time/residue: 0.2342 time to fit residues: 60.9487 Evaluate side-chains 186 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN E 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119273 restraints weight = 13299.064| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.24 r_work: 0.3046 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 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 = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9035 Z= 0.284 Angle : 0.533 7.928 12169 Z= 0.277 Chirality : 0.039 0.146 1447 Planarity : 0.004 0.056 1544 Dihedral : 3.599 13.079 1223 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.55 % Allowed : 23.27 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.24), residues: 1149 helix: 2.46 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.66 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.005 0.001 HIS D 136 PHE 0.017 0.002 PHE G 143 TYR 0.007 0.001 TYR E 188 ARG 0.006 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 148 ASP cc_start: 0.7844 (m-30) cc_final: 0.7625 (m-30) REVERT: C 219 MET cc_start: 0.6313 (ttp) cc_final: 0.5698 (ttt) REVERT: E 249 LEU cc_start: 0.7694 (pt) cc_final: 0.7328 (pp) REVERT: F 20 MET cc_start: 0.2912 (ptm) cc_final: 0.1797 (tpt) REVERT: F 69 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7783 (mttt) REVERT: F 105 MET cc_start: 0.8263 (tpt) cc_final: 0.7693 (ttp) outliers start: 24 outliers final: 10 residues processed: 197 average time/residue: 0.2383 time to fit residues: 63.0344 Evaluate side-chains 190 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 GLN E 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.181581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124211 restraints weight = 16228.613| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.23 r_work: 0.3068 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9035 Z= 0.151 Angle : 0.463 8.093 12169 Z= 0.241 Chirality : 0.036 0.146 1447 Planarity : 0.004 0.049 1544 Dihedral : 3.439 14.058 1223 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.02 % Allowed : 23.49 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.25), residues: 1149 helix: 2.72 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.70 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.001 HIS E 116 PHE 0.012 0.001 PHE E 143 TYR 0.011 0.001 TYR E 237 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.7269 (mt0) cc_final: 0.6694 (mt0) REVERT: C 179 MET cc_start: 0.7980 (ptm) cc_final: 0.7708 (ttt) REVERT: C 219 MET cc_start: 0.6747 (ttp) cc_final: 0.6121 (ttt) REVERT: D 207 ARG cc_start: 0.8969 (tpt-90) cc_final: 0.8719 (tpp80) REVERT: D 208 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7941 (ttp-170) REVERT: E 249 LEU cc_start: 0.7827 (pt) cc_final: 0.7424 (pp) REVERT: F 20 MET cc_start: 0.2351 (ptm) cc_final: 0.1505 (tpt) REVERT: F 69 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7789 (mttt) REVERT: F 105 MET cc_start: 0.8186 (tpt) cc_final: 0.7787 (ttp) outliers start: 19 outliers final: 12 residues processed: 197 average time/residue: 0.2454 time to fit residues: 64.4812 Evaluate side-chains 188 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.185185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129137 restraints weight = 17078.819| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.25 r_work: 0.3058 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9035 Z= 0.168 Angle : 0.481 9.238 12169 Z= 0.247 Chirality : 0.036 0.180 1447 Planarity : 0.004 0.045 1544 Dihedral : 3.414 13.947 1223 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.13 % Allowed : 24.44 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.24), residues: 1149 helix: 2.84 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : -0.60 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 PHE 0.013 0.001 PHE E 143 TYR 0.016 0.001 TYR E 237 ARG 0.006 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 179 MET cc_start: 0.7873 (ptm) cc_final: 0.7594 (ttt) REVERT: C 219 MET cc_start: 0.6497 (ttp) cc_final: 0.5837 (ttt) REVERT: D 102 ASN cc_start: 0.7850 (t0) cc_final: 0.7644 (t0) REVERT: D 207 ARG cc_start: 0.8987 (tpt-90) cc_final: 0.8751 (tpp80) REVERT: D 208 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7948 (ttp-170) REVERT: E 72 GLU cc_start: 0.7728 (pm20) cc_final: 0.7109 (tt0) REVERT: E 249 LEU cc_start: 0.7818 (pt) cc_final: 0.7460 (pp) REVERT: F 20 MET cc_start: 0.1974 (ptm) cc_final: 0.1221 (tpt) REVERT: F 69 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7776 (mttt) REVERT: F 105 MET cc_start: 0.8222 (tpt) cc_final: 0.7785 (ttp) REVERT: F 235 ASP cc_start: 0.6678 (m-30) cc_final: 0.6112 (t0) REVERT: G 105 MET cc_start: 0.6979 (tmm) cc_final: 0.6708 (tmm) outliers start: 20 outliers final: 15 residues processed: 200 average time/residue: 0.2480 time to fit residues: 65.7053 Evaluate side-chains 197 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 0.0070 chunk 76 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.181390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130172 restraints weight = 17338.830| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.34 r_work: 0.3096 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9035 Z= 0.148 Angle : 0.468 8.091 12169 Z= 0.239 Chirality : 0.036 0.160 1447 Planarity : 0.003 0.042 1544 Dihedral : 3.371 14.389 1223 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.23 % Allowed : 23.91 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.25), residues: 1149 helix: 2.90 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.74 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 PHE 0.012 0.001 PHE F 143 TYR 0.012 0.001 TYR E 237 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 ILE cc_start: 0.8033 (mt) cc_final: 0.7809 (mt) REVERT: C 179 MET cc_start: 0.7787 (ptm) cc_final: 0.7524 (ttt) REVERT: C 219 MET cc_start: 0.6618 (ttp) cc_final: 0.6129 (ttt) REVERT: D 28 MET cc_start: 0.6707 (ttp) cc_final: 0.6405 (ttm) REVERT: D 207 ARG cc_start: 0.8974 (tpt-90) cc_final: 0.8728 (tpp80) REVERT: D 208 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7962 (ttp-170) REVERT: E 128 ASP cc_start: 0.7802 (t0) cc_final: 0.7025 (t0) REVERT: F 20 MET cc_start: 0.2449 (ptm) cc_final: 0.1695 (tpt) REVERT: F 69 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7761 (mttt) REVERT: F 105 MET cc_start: 0.8216 (tpt) cc_final: 0.7842 (ttp) REVERT: F 235 ASP cc_start: 0.6673 (m-30) cc_final: 0.6106 (t0) REVERT: G 105 MET cc_start: 0.6992 (tmm) cc_final: 0.6739 (tmm) outliers start: 21 outliers final: 16 residues processed: 207 average time/residue: 0.2479 time to fit residues: 67.9177 Evaluate side-chains 203 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131094 restraints weight = 16180.860| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.01 r_work: 0.3137 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9035 Z= 0.148 Angle : 0.478 7.795 12169 Z= 0.245 Chirality : 0.036 0.189 1447 Planarity : 0.004 0.041 1544 Dihedral : 3.372 14.370 1223 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 24.44 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.25), residues: 1149 helix: 2.93 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.73 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 PHE 0.012 0.001 PHE F 143 TYR 0.004 0.001 TYR D 241 ARG 0.007 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8020 (mp) REVERT: C 37 ILE cc_start: 0.8044 (mt) cc_final: 0.7797 (mt) REVERT: C 179 MET cc_start: 0.7691 (ptm) cc_final: 0.7456 (ttt) REVERT: C 219 MET cc_start: 0.6294 (ttp) cc_final: 0.5856 (ttt) REVERT: D 28 MET cc_start: 0.6602 (ttp) cc_final: 0.6272 (ttm) REVERT: D 207 ARG cc_start: 0.8936 (tpt-90) cc_final: 0.8693 (tpp80) REVERT: D 208 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7868 (ttp-170) REVERT: E 72 GLU cc_start: 0.7644 (pm20) cc_final: 0.7202 (tt0) REVERT: E 128 ASP cc_start: 0.7808 (t0) cc_final: 0.7036 (t0) REVERT: E 249 LEU cc_start: 0.7760 (pt) cc_final: 0.7378 (pp) REVERT: F 20 MET cc_start: 0.2460 (ptm) cc_final: 0.1794 (tpt) REVERT: F 69 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7745 (mttt) REVERT: F 105 MET cc_start: 0.8281 (tpt) cc_final: 0.7819 (ttp) REVERT: F 235 ASP cc_start: 0.6576 (m-30) cc_final: 0.6079 (t0) REVERT: G 68 PHE cc_start: 0.7625 (m-80) cc_final: 0.7424 (m-80) REVERT: G 105 MET cc_start: 0.7004 (tmm) cc_final: 0.6727 (tmm) outliers start: 18 outliers final: 16 residues processed: 204 average time/residue: 0.2452 time to fit residues: 66.1251 Evaluate side-chains 207 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.179599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129802 restraints weight = 17292.058| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.31 r_work: 0.3034 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 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 = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9035 Z= 0.213 Angle : 0.513 8.288 12169 Z= 0.263 Chirality : 0.037 0.187 1447 Planarity : 0.004 0.042 1544 Dihedral : 3.466 13.619 1223 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.23 % Allowed : 24.44 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.25), residues: 1149 helix: 2.78 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.82 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.003 0.001 HIS D 136 PHE 0.014 0.001 PHE F 143 TYR 0.006 0.001 TYR E 188 ARG 0.004 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 67 MET cc_start: 0.7647 (mtt) cc_final: 0.7442 (mmt) REVERT: C 179 MET cc_start: 0.8008 (ptm) cc_final: 0.7681 (ttt) REVERT: C 219 MET cc_start: 0.6427 (ttp) cc_final: 0.6009 (ttt) REVERT: D 28 MET cc_start: 0.6738 (ttp) cc_final: 0.6436 (ttm) REVERT: D 207 ARG cc_start: 0.9013 (tpt-90) cc_final: 0.8771 (tpp80) REVERT: D 208 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8044 (ttp-170) REVERT: E 72 GLU cc_start: 0.7733 (pm20) cc_final: 0.7215 (tt0) REVERT: E 128 ASP cc_start: 0.7887 (t0) cc_final: 0.7134 (t0) REVERT: F 20 MET cc_start: 0.2478 (ptm) cc_final: 0.1762 (tpt) REVERT: F 69 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7760 (mttt) REVERT: F 105 MET cc_start: 0.8353 (tpt) cc_final: 0.7864 (ttp) REVERT: F 235 ASP cc_start: 0.6762 (m-30) cc_final: 0.6273 (t0) REVERT: G 105 MET cc_start: 0.6977 (tmm) cc_final: 0.6716 (tmm) outliers start: 21 outliers final: 18 residues processed: 197 average time/residue: 0.2442 time to fit residues: 64.1498 Evaluate side-chains 201 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 102 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125769 restraints weight = 13454.752| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.88 r_work: 0.3161 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9035 Z= 0.166 Angle : 0.496 9.235 12169 Z= 0.253 Chirality : 0.036 0.177 1447 Planarity : 0.004 0.041 1544 Dihedral : 3.419 14.095 1223 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 24.97 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.25), residues: 1149 helix: 2.86 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.80 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 PHE 0.012 0.001 PHE E 143 TYR 0.006 0.001 TYR D 188 ARG 0.008 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8722 (tpp) cc_final: 0.8183 (ttt) REVERT: C 36 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8183 (mp) REVERT: C 67 MET cc_start: 0.7626 (mtt) cc_final: 0.7420 (mmt) REVERT: C 179 MET cc_start: 0.7996 (ptm) cc_final: 0.7748 (ttt) REVERT: C 219 MET cc_start: 0.6637 (ttp) cc_final: 0.6205 (ttt) REVERT: D 28 MET cc_start: 0.6677 (ttp) cc_final: 0.6373 (ttm) REVERT: D 207 ARG cc_start: 0.9037 (tpt-90) cc_final: 0.8810 (tpp80) REVERT: D 208 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8047 (ttp-170) REVERT: E 72 GLU cc_start: 0.7514 (pm20) cc_final: 0.6857 (tt0) REVERT: E 74 GLU cc_start: 0.8157 (mp0) cc_final: 0.7495 (mp0) REVERT: E 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7115 (t0) REVERT: F 20 MET cc_start: 0.2397 (ptm) cc_final: 0.2009 (tmm) REVERT: F 67 MET cc_start: 0.8623 (ptt) cc_final: 0.8295 (ptt) REVERT: F 69 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7727 (mttt) REVERT: F 105 MET cc_start: 0.8273 (tpt) cc_final: 0.7849 (ttp) REVERT: F 116 HIS cc_start: 0.7065 (m-70) cc_final: 0.6182 (m90) REVERT: F 235 ASP cc_start: 0.6807 (m-30) cc_final: 0.6255 (t0) REVERT: G 105 MET cc_start: 0.6948 (tmm) cc_final: 0.6685 (tmm) outliers start: 18 outliers final: 16 residues processed: 194 average time/residue: 0.2279 time to fit residues: 59.2753 Evaluate side-chains 198 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 0.0060 chunk 113 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.0070 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.181472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122457 restraints weight = 17483.972| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.54 r_work: 0.3116 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9035 Z= 0.141 Angle : 0.485 10.019 12169 Z= 0.247 Chirality : 0.036 0.192 1447 Planarity : 0.004 0.041 1544 Dihedral : 3.375 14.584 1223 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.49 % Allowed : 24.65 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.25), residues: 1149 helix: 2.94 (0.16), residues: 1007 sheet: None (None), residues: 0 loop : -0.65 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.001 0.000 HIS E 116 PHE 0.011 0.001 PHE E 143 TYR 0.005 0.001 TYR D 188 ARG 0.008 0.000 ARG E 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8710 (tpp) cc_final: 0.8244 (ttt) REVERT: C 37 ILE cc_start: 0.7939 (mt) cc_final: 0.7647 (mt) REVERT: C 219 MET cc_start: 0.6693 (ttp) cc_final: 0.6350 (ttt) REVERT: D 28 MET cc_start: 0.6608 (ttp) cc_final: 0.6304 (ttm) REVERT: D 207 ARG cc_start: 0.8950 (tpt-90) cc_final: 0.8715 (tpp80) REVERT: D 208 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7876 (ttp-170) REVERT: E 72 GLU cc_start: 0.7454 (pm20) cc_final: 0.6838 (tt0) REVERT: E 74 GLU cc_start: 0.8022 (mp0) cc_final: 0.7677 (mp0) REVERT: E 83 MET cc_start: 0.6991 (mmp) cc_final: 0.6344 (mmm) REVERT: E 128 ASP cc_start: 0.7785 (t0) cc_final: 0.7072 (t0) REVERT: E 179 MET cc_start: 0.8466 (tpt) cc_final: 0.8191 (tpp) REVERT: F 20 MET cc_start: 0.2553 (ptm) cc_final: 0.1973 (tpp) REVERT: F 31 ASP cc_start: 0.6654 (m-30) cc_final: 0.5665 (m-30) REVERT: F 69 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7630 (mttm) REVERT: F 105 MET cc_start: 0.8220 (tpt) cc_final: 0.7802 (ttp) REVERT: F 116 HIS cc_start: 0.7037 (m-70) cc_final: 0.6145 (m90) REVERT: F 235 ASP cc_start: 0.6685 (m-30) cc_final: 0.6130 (t0) REVERT: G 68 PHE cc_start: 0.7485 (m-80) cc_final: 0.7275 (m-80) REVERT: G 105 MET cc_start: 0.6915 (tmm) cc_final: 0.6651 (tmm) outliers start: 14 outliers final: 11 residues processed: 195 average time/residue: 0.2445 time to fit residues: 63.1032 Evaluate side-chains 195 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 0.0670 chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.179226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122871 restraints weight = 12026.124| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.14 r_work: 0.3135 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9035 Z= 0.212 Angle : 0.532 8.721 12169 Z= 0.270 Chirality : 0.038 0.208 1447 Planarity : 0.004 0.042 1544 Dihedral : 3.465 13.648 1223 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 24.97 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.25), residues: 1149 helix: 2.79 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.74 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 18 HIS 0.006 0.001 HIS E 116 PHE 0.014 0.001 PHE G 143 TYR 0.013 0.001 TYR E 237 ARG 0.005 0.000 ARG E 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4931.22 seconds wall clock time: 88 minutes 2.26 seconds (5282.26 seconds total)