Starting phenix.real_space_refine on Thu Mar 13 06:32:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zz0_60585/03_2025/8zz0_60585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zz0_60585/03_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_60585/03_2025/8zz0_60585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zz0_60585/03_2025/8zz0_60585.map" model { file = "/net/cci-nas-00/data/ceres_data/8zz0_60585/03_2025/8zz0_60585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zz0_60585/03_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-5624/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: 6.18, per 1000 atoms: 0.69 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 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: 0.81 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: 2.69 Time building geometry restraints manager: 2.51 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.320 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- 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 : 0.994 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: 0.2330 time to fit residues: 56.0629 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 : 0.907 ------------------------------------------------------------------------------- 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 = 0.153141 restraints weight = 11576.937| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.94 r_work: 0.3041 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 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 = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 1.061 Fit side-chains revert: symmetry clash REVERT: C 219 MET cc_start: 0.6395 (ttp) cc_final: 0.5865 (ttt) REVERT: E 169 MET cc_start: 0.8256 (tpp) cc_final: 0.7906 (ttm) REVERT: F 20 MET cc_start: 0.2400 (ptm) cc_final: 0.1411 (tpt) REVERT: F 105 MET cc_start: 0.8110 (tpt) cc_final: 0.7550 (ttp) REVERT: F 173 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7092 (tttm) outliers start: 16 outliers final: 10 residues processed: 194 average time/residue: 0.2322 time to fit residues: 60.4342 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 : 0.918 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 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: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.182302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127026 restraints weight = 13069.931| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.99 r_work: 0.3009 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9035 Z= 0.315 Angle : 0.557 7.502 12169 Z= 0.290 Chirality : 0.040 0.147 1447 Planarity : 0.004 0.057 1544 Dihedral : 3.699 13.407 1223 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.76 % Allowed : 22.85 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.24), residues: 1149 helix: 2.30 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -1.09 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 18 HIS 0.007 0.002 HIS D 136 PHE 0.019 0.002 PHE G 143 TYR 0.009 0.001 TYR E 188 ARG 0.005 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 212 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7993 (mp) REVERT: C 148 ASP cc_start: 0.7946 (m-30) cc_final: 0.7693 (m-30) REVERT: C 219 MET cc_start: 0.6326 (ttp) cc_final: 0.5687 (ttt) REVERT: D 208 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7894 (ttp-170) REVERT: E 249 LEU cc_start: 0.7794 (pt) cc_final: 0.7343 (pp) REVERT: F 20 MET cc_start: 0.2826 (ptm) cc_final: 0.1718 (tpt) REVERT: F 69 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7808 (mttt) REVERT: F 105 MET cc_start: 0.8246 (tpt) cc_final: 0.7676 (ttp) REVERT: F 168 ASN cc_start: 0.7946 (m110) cc_final: 0.7631 (m110) REVERT: F 235 ASP cc_start: 0.6828 (m-30) cc_final: 0.6252 (t0) REVERT: G 56 PHE cc_start: 0.8781 (m-10) cc_final: 0.8526 (m-80) outliers start: 26 outliers final: 15 residues processed: 199 average time/residue: 0.2392 time to fit residues: 63.4532 Evaluate side-chains 191 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 153 MET 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 E residue 105 MET Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 155 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- 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 ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130050 restraints weight = 15932.692| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.27 r_work: 0.3055 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9035 Z= 0.165 Angle : 0.475 8.035 12169 Z= 0.246 Chirality : 0.036 0.146 1447 Planarity : 0.004 0.050 1544 Dihedral : 3.502 14.065 1223 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.81 % Allowed : 23.70 % 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: 3.46 (0.24), residues: 1149 helix: 2.66 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.64 (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 D 136 PHE 0.013 0.001 PHE E 143 TYR 0.005 0.001 TYR F 188 ARG 0.005 0.000 ARG E 216 *********************** 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 202 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 148 ASP cc_start: 0.7880 (m-30) cc_final: 0.7678 (m-30) REVERT: C 179 MET cc_start: 0.7857 (ptm) cc_final: 0.7588 (ttt) REVERT: C 219 MET cc_start: 0.6658 (ttp) cc_final: 0.5998 (ttt) REVERT: D 28 MET cc_start: 0.7180 (ptp) cc_final: 0.6939 (ptm) REVERT: D 207 ARG cc_start: 0.8961 (tpt-90) cc_final: 0.8706 (tpp80) REVERT: D 208 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7962 (ttp-170) REVERT: E 52 MET cc_start: 0.7904 (tpp) cc_final: 0.7559 (tpp) REVERT: E 249 LEU cc_start: 0.7785 (pt) cc_final: 0.7406 (pp) REVERT: F 20 MET cc_start: 0.2507 (ptm) cc_final: 0.1596 (tpt) REVERT: F 69 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7801 (mttt) REVERT: F 105 MET cc_start: 0.8218 (tpt) cc_final: 0.7806 (ttp) REVERT: F 235 ASP cc_start: 0.6705 (m-30) cc_final: 0.6094 (t0) outliers start: 17 outliers final: 11 residues processed: 192 average time/residue: 0.2402 time to fit residues: 61.7724 Evaluate side-chains 187 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.182948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126757 restraints weight = 17047.602| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.23 r_work: 0.3014 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1882 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= 0.218 Angle : 0.506 9.381 12169 Z= 0.259 Chirality : 0.037 0.155 1447 Planarity : 0.004 0.047 1544 Dihedral : 3.527 13.534 1223 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.34 % Allowed : 24.34 % 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: 3.45 (0.25), residues: 1149 helix: 2.65 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.63 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS D 136 PHE 0.014 0.001 PHE E 143 TYR 0.018 0.001 TYR E 237 ARG 0.005 0.000 ARG C 247 *********************** 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 207 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8185 (ttp) cc_final: 0.7830 (tmm) REVERT: C 179 MET cc_start: 0.7995 (ptm) cc_final: 0.7674 (ttt) REVERT: C 219 MET cc_start: 0.6555 (ttp) cc_final: 0.6019 (ttt) REVERT: D 28 MET cc_start: 0.7007 (ptp) cc_final: 0.6767 (ptm) REVERT: D 207 ARG cc_start: 0.8993 (tpt-90) cc_final: 0.8762 (tpp80) REVERT: D 208 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8013 (ttp-170) REVERT: E 128 ASP cc_start: 0.7885 (t0) cc_final: 0.7077 (t0) REVERT: F 20 MET cc_start: 0.2604 (ptm) cc_final: 0.1631 (tpt) REVERT: F 69 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7789 (mttt) REVERT: F 105 MET cc_start: 0.8239 (tpt) cc_final: 0.7850 (ttp) REVERT: F 195 MET cc_start: 0.8938 (mtm) cc_final: 0.8728 (mtm) REVERT: F 235 ASP cc_start: 0.6789 (m-30) cc_final: 0.6245 (t0) REVERT: G 56 PHE cc_start: 0.8832 (m-80) cc_final: 0.8333 (m-80) outliers start: 22 outliers final: 13 residues processed: 198 average time/residue: 0.2433 time to fit residues: 65.1314 Evaluate side-chains 191 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 F residue 49 LYS Chi-restraints excluded: chain F residue 103 THR 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: 6.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.178123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136306 restraints weight = 17272.768| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.23 r_work: 0.3129 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.149 Angle : 0.471 8.283 12169 Z= 0.242 Chirality : 0.036 0.181 1447 Planarity : 0.004 0.044 1544 Dihedral : 3.434 14.340 1223 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.13 % Allowed : 24.34 % Favored : 73.54 % 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: 3.76 (0.25), residues: 1149 helix: 2.88 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : -0.54 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS E 116 PHE 0.013 0.001 PHE E 143 TYR 0.011 0.001 TYR E 237 ARG 0.007 0.000 ARG E 216 *********************** 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 216 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 179 MET cc_start: 0.7763 (ptm) cc_final: 0.7517 (ttt) REVERT: C 219 MET cc_start: 0.6635 (ttp) cc_final: 0.6211 (ttt) REVERT: D 28 MET cc_start: 0.6729 (ptp) cc_final: 0.6513 (ptm) REVERT: D 207 ARG cc_start: 0.8937 (tpt-90) cc_final: 0.8685 (tpp80) REVERT: D 208 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7928 (ttp-170) REVERT: E 72 GLU cc_start: 0.7747 (pm20) cc_final: 0.7146 (tt0) REVERT: E 128 ASP cc_start: 0.7859 (t0) cc_final: 0.7080 (t0) REVERT: F 20 MET cc_start: 0.2781 (ptm) cc_final: 0.2053 (tpp) REVERT: F 69 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7726 (mttt) REVERT: F 105 MET cc_start: 0.8320 (tpt) cc_final: 0.7944 (ttp) REVERT: F 235 ASP cc_start: 0.6745 (m-30) cc_final: 0.6304 (t0) outliers start: 20 outliers final: 14 residues processed: 208 average time/residue: 0.2832 time to fit residues: 78.4888 Evaluate side-chains 199 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 175 ILE 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 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: 3.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.174488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138661 restraints weight = 16145.857| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.91 r_work: 0.3117 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.004 0.044 9035 Z= 0.228 Angle : 0.512 7.994 12169 Z= 0.263 Chirality : 0.038 0.176 1447 Planarity : 0.004 0.044 1544 Dihedral : 3.524 13.544 1223 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 24.12 % 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: 3.51 (0.24), residues: 1149 helix: 2.73 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.85 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 18 HIS 0.004 0.001 HIS D 136 PHE 0.015 0.001 PHE G 143 TYR 0.007 0.001 TYR E 188 ARG 0.005 0.000 ARG E 216 *********************** 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 211 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 179 MET cc_start: 0.7818 (ptm) cc_final: 0.7503 (ttt) REVERT: C 219 MET cc_start: 0.6634 (ttp) cc_final: 0.6218 (ttt) REVERT: D 28 MET cc_start: 0.6848 (ptp) cc_final: 0.6569 (ptm) REVERT: D 207 ARG cc_start: 0.8914 (tpt-90) cc_final: 0.8662 (tpp80) REVERT: D 208 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7920 (ttp-170) REVERT: E 74 GLU cc_start: 0.8171 (mp0) cc_final: 0.7788 (mp0) REVERT: E 128 ASP cc_start: 0.7851 (t0) cc_final: 0.7020 (t0) REVERT: F 69 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7729 (mttt) REVERT: F 105 MET cc_start: 0.8255 (tpt) cc_final: 0.7853 (ttp) REVERT: F 235 ASP cc_start: 0.7063 (m-30) cc_final: 0.6696 (t0) REVERT: G 56 PHE cc_start: 0.8820 (m-80) cc_final: 0.8305 (m-80) REVERT: G 105 MET cc_start: 0.6989 (tmm) cc_final: 0.6663 (tmm) outliers start: 24 outliers final: 17 residues processed: 200 average time/residue: 0.2440 time to fit residues: 64.7287 Evaluate side-chains 196 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL 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 175 ILE Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 ILE 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 212 THR Chi-restraints excluded: chain G residue 35 ILE 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: 1.9990 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.184531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127982 restraints weight = 17019.902| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.31 r_work: 0.3022 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9035 Z= 0.207 Angle : 0.502 7.621 12169 Z= 0.258 Chirality : 0.037 0.196 1447 Planarity : 0.004 0.044 1544 Dihedral : 3.537 13.789 1223 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.55 % Allowed : 24.55 % Favored : 72.90 % 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: 3.59 (0.24), residues: 1149 helix: 2.76 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -0.49 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.007 0.001 HIS E 116 PHE 0.014 0.001 PHE E 143 TYR 0.006 0.001 TYR E 188 ARG 0.006 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: 24 poor density : 182 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 MET cc_start: 0.7679 (mtt) cc_final: 0.7424 (mmt) REVERT: C 179 MET cc_start: 0.7939 (ptm) cc_final: 0.7668 (ttt) REVERT: D 28 MET cc_start: 0.6876 (ptp) cc_final: 0.6301 (ptp) REVERT: D 207 ARG cc_start: 0.8977 (tpt-90) cc_final: 0.8744 (tpp80) REVERT: D 208 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8007 (ttp-170) REVERT: E 128 ASP cc_start: 0.7870 (t0) cc_final: 0.7030 (t0) REVERT: F 67 MET cc_start: 0.8574 (ptt) cc_final: 0.8248 (ptt) REVERT: F 69 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7684 (mttm) REVERT: F 105 MET cc_start: 0.8167 (tpt) cc_final: 0.7832 (ttp) REVERT: F 235 ASP cc_start: 0.7111 (m-30) cc_final: 0.6697 (t0) REVERT: G 56 PHE cc_start: 0.8844 (m-80) cc_final: 0.8337 (m-80) REVERT: G 105 MET cc_start: 0.6868 (tmm) cc_final: 0.6578 (tmm) outliers start: 24 outliers final: 18 residues processed: 197 average time/residue: 0.2247 time to fit residues: 59.5572 Evaluate side-chains 197 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 61 ILE Chi-restraints excluded: chain C residue 158 THR 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 175 ILE Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 ILE 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 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: 3.9990 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 102 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.187071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131451 restraints weight = 13178.062| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.21 r_work: 0.3077 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9035 Z= 0.158 Angle : 0.503 10.188 12169 Z= 0.255 Chirality : 0.036 0.193 1447 Planarity : 0.004 0.043 1544 Dihedral : 3.474 14.521 1223 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.70 % Allowed : 25.19 % 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: 3.75 (0.25), residues: 1149 helix: 2.89 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -0.65 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.007 0.001 HIS E 116 PHE 0.014 0.001 PHE G 44 TYR 0.004 0.001 TYR E 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 205 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 MET cc_start: 0.7590 (mtt) cc_final: 0.7385 (mmt) REVERT: C 179 MET cc_start: 0.7681 (ptm) cc_final: 0.7481 (ttt) REVERT: D 28 MET cc_start: 0.6762 (ptp) cc_final: 0.6509 (ptm) REVERT: D 207 ARG cc_start: 0.8919 (tpt-90) cc_final: 0.8691 (tpp80) REVERT: D 208 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7901 (ttp-170) REVERT: E 74 GLU cc_start: 0.8082 (mp0) cc_final: 0.7416 (mp0) REVERT: E 128 ASP cc_start: 0.7781 (t0) cc_final: 0.6994 (t0) REVERT: F 20 MET cc_start: 0.2586 (ptm) cc_final: 0.2154 (tmm) REVERT: F 31 ASP cc_start: 0.6746 (m-30) cc_final: 0.6204 (m-30) REVERT: F 69 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7727 (mttt) REVERT: F 105 MET cc_start: 0.8068 (tpt) cc_final: 0.7798 (ttp) REVERT: F 116 HIS cc_start: 0.6613 (m-70) cc_final: 0.5900 (m90) REVERT: F 235 ASP cc_start: 0.7079 (m-30) cc_final: 0.6618 (t0) REVERT: G 105 MET cc_start: 0.6895 (tmm) cc_final: 0.6579 (tmm) outliers start: 16 outliers final: 13 residues processed: 197 average time/residue: 0.2463 time to fit residues: 64.5461 Evaluate side-chains 196 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 61 ILE Chi-restraints excluded: chain C residue 158 THR 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 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 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: 5.9990 chunk 49 optimal weight: 2.9990 chunk 113 optimal weight: 0.0010 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.186587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134137 restraints weight = 17206.935| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.38 r_work: 0.3050 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9035 Z= 0.142 Angle : 0.488 10.663 12169 Z= 0.249 Chirality : 0.036 0.190 1447 Planarity : 0.004 0.043 1544 Dihedral : 3.443 15.052 1223 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.59 % Allowed : 25.29 % 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: 3.94 (0.25), residues: 1149 helix: 3.00 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.36 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.007 0.001 HIS E 116 PHE 0.014 0.001 PHE G 44 TYR 0.006 0.001 TYR D 188 ARG 0.007 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 208 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8029 (mt) cc_final: 0.7805 (mp) REVERT: C 37 ILE cc_start: 0.8169 (mt) cc_final: 0.7937 (mt) REVERT: D 28 MET cc_start: 0.6666 (ptp) cc_final: 0.6218 (ptp) REVERT: D 207 ARG cc_start: 0.9050 (tpt-90) cc_final: 0.8818 (tpp80) REVERT: D 208 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8009 (ttp-170) REVERT: E 128 ASP cc_start: 0.7835 (t0) cc_final: 0.7048 (t0) REVERT: F 20 MET cc_start: 0.2845 (ptm) cc_final: 0.2170 (tmm) REVERT: F 31 ASP cc_start: 0.6768 (m-30) cc_final: 0.6110 (m-30) REVERT: F 69 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7728 (mttt) REVERT: F 105 MET cc_start: 0.8164 (tpt) cc_final: 0.7851 (ttp) REVERT: F 116 HIS cc_start: 0.7165 (m-70) cc_final: 0.6255 (m90) REVERT: F 235 ASP cc_start: 0.7170 (m-30) cc_final: 0.6721 (t0) REVERT: G 68 PHE cc_start: 0.7571 (m-80) cc_final: 0.7356 (m-80) REVERT: G 105 MET cc_start: 0.6920 (tmm) cc_final: 0.6636 (tmm) outliers start: 15 outliers final: 11 residues processed: 201 average time/residue: 0.2426 time to fit residues: 65.0415 Evaluate side-chains 200 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL 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 E residue 49 LYS Chi-restraints excluded: chain E residue 103 THR 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 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: 6.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.181039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137751 restraints weight = 11973.719| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.78 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9035 Z= 0.179 Angle : 0.513 8.920 12169 Z= 0.262 Chirality : 0.037 0.196 1447 Planarity : 0.004 0.043 1544 Dihedral : 3.442 14.228 1223 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.28 % Allowed : 25.19 % Favored : 73.54 % 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: 3.88 (0.25), residues: 1149 helix: 2.96 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.39 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.007 0.001 HIS E 116 PHE 0.014 0.001 PHE D 44 TYR 0.011 0.001 TYR E 237 ARG 0.006 0.000 ARG E 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5054.58 seconds wall clock time: 89 minutes 16.55 seconds (5356.55 seconds total)