Starting phenix.real_space_refine on Fri Jul 3 22:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zxy_15017/07_2026/7zxy_15017.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 10361 2.51 5 N 2417 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15606 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1750 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "B" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1211 Classifications: {'peptide': 158} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 140} Chain: "C" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2116 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "D" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1248 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 1 Chain: "E" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 267 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "H" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 235 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1750 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "J" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2116 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1248 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 1 Chain: "M" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "P" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 235 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'ECH': 1, 'HEC': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'CLA': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'HEC': 1, 'LFA': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 221 Unusual residues: {'ECH': 1, 'HEC': 1, 'HEM': 2, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 211 Unusual residues: {'CLA': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5796 SG CYS D 120 78.989 77.612 95.772 1.00 30.79 S ATOM 5936 SG CYS D 138 76.370 80.248 96.868 1.00 33.12 S ATOM 13144 SG CYS L 120 34.375 76.130 50.594 1.00 30.90 S ATOM 13284 SG CYS L 138 37.537 74.579 48.855 1.00 31.82 S Time building chain proxies: 3.52, per 1000 atoms: 0.23 Number of scatterers: 15606 At special positions: 0 Unit cell: (114.48, 128.26, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 76 16.00 P 7 15.00 Mg 2 11.99 O 2731 8.00 N 2417 7.00 C 10361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 140 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 597.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 122 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 120 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 141 " pdb=" FES L 201 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 141 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 122 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 138 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 120 " Number of angles added : 6 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 17 sheets defined 49.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.917A pdb=" N GLY A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 39 through 58 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.993A pdb=" N ILE B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 147 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 21 through 26 removed outlier: 4.149A pdb=" N CYS C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 247 through 283 Processing helix chain 'D' and resid 24 through 55 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.549A pdb=" N GLY E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 32 Processing helix chain 'G' and resid 3 through 30 Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 3 through 26 Processing helix chain 'I' and resid 11 through 20 removed outlier: 4.007A pdb=" N PHE I 15 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG I 18 " --> pdb=" O TRP I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 removed outlier: 4.044A pdb=" N ILE I 24 " --> pdb=" O GLU I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 41 Processing helix chain 'I' and resid 42 through 62 Processing helix chain 'I' and resid 71 through 82 Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 121 through 144 removed outlier: 3.871A pdb=" N SER I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 160 removed outlier: 3.655A pdb=" N GLY I 160 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 Processing helix chain 'I' and resid 168 through 178 Processing helix chain 'I' and resid 183 through 196 Processing helix chain 'I' and resid 196 through 217 Processing helix chain 'J' and resid 11 through 21 Processing helix chain 'J' and resid 39 through 58 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.519A pdb=" N LEU J 91 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 109 removed outlier: 3.971A pdb=" N ILE J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 20 through 25 removed outlier: 3.622A pdb=" N CYS K 25 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 247 through 284 Processing helix chain 'L' and resid 24 through 55 Proline residue: L 49 - end of helix Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'M' and resid 2 through 29 Processing helix chain 'N' and resid 7 through 33 removed outlier: 3.734A pdb=" N GLY N 33 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 30 Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 26 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.635A pdb=" N VAL C 49 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.548A pdb=" N HIS C 150 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA C 74 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLY C 117 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 76 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE C 115 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67 removed outlier: 4.107A pdb=" N VAL D 66 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 89 through 94 removed outlier: 3.709A pdb=" N VAL D 91 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 116 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB1, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AB2, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=AB3, first strand: chain 'K' and resid 39 through 40 removed outlier: 6.820A pdb=" N ALA K 74 " --> pdb=" O GLY K 117 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY K 117 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU K 76 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE K 115 " --> pdb=" O LEU K 76 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'K' and resid 178 through 179 Processing sheet with id=AB6, first strand: chain 'K' and resid 191 through 193 Processing sheet with id=AB7, first strand: chain 'L' and resid 90 through 94 removed outlier: 4.857A pdb=" N VAL L 104 " --> pdb=" O TYR L 114 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR L 114 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 129 through 130 removed outlier: 6.303A pdb=" N GLN L 144 " --> pdb=" O VAL L 152 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2298 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: 2.06 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6385 1.41 - 1.61: 9459 1.61 - 1.81: 132 1.81 - 2.01: 8 2.01 - 2.20: 48 Bond restraints: 16032 Sorted by residual: bond pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC I 305 " pdb=" C3D HEC I 305 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC A 304 " pdb=" C3D HEC A 304 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAC HEC A 304 " pdb=" CBC HEC A 304 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 21544 3.27 - 6.53: 292 6.53 - 9.80: 28 9.80 - 13.07: 13 13.07 - 16.33: 11 Bond angle restraints: 21888 Sorted by residual: angle pdb=" C3C HEC I 305 " pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sigma weight residual 109.00 125.33 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" C3B HEC I 305 " pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sigma weight residual 109.00 124.21 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O11 PGV B 202 " pdb=" P PGV B 202 " pdb=" O12 PGV B 202 " ideal model delta sigma weight residual 92.97 107.50 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C3B HEC A 304 " pdb=" CAB HEC A 304 " pdb=" CBB HEC A 304 " ideal model delta sigma weight residual 109.00 123.45 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C3C HEC A 304 " pdb=" CAC HEC A 304 " pdb=" CBC HEC A 304 " ideal model delta sigma weight residual 109.00 123.38 -14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 21883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 8945 32.91 - 65.82: 201 65.82 - 98.74: 34 98.74 - 131.65: 2 131.65 - 164.56: 3 Dihedral angle restraints: 9185 sinusoidal: 3784 harmonic: 5401 Sorted by residual: dihedral pdb=" C2B HEC A 304 " pdb=" C3B HEC A 304 " pdb=" CAB HEC A 304 " pdb=" CBB HEC A 304 " ideal model delta sinusoidal sigma weight residual 60.00 -29.50 89.50 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2B HEC I 305 " pdb=" C3B HEC I 305 " pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sinusoidal sigma weight residual 60.00 -21.71 81.71 2 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" C2C HEC I 305 " pdb=" C3C HEC I 305 " pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sinusoidal sigma weight residual 60.00 0.17 59.83 2 1.00e+01 1.00e-02 3.59e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1786 0.047 - 0.095: 477 0.095 - 0.142: 107 0.142 - 0.189: 8 0.189 - 0.237: 7 Chirality restraints: 2385 Sorted by residual: chirality pdb=" C05 PGV C 303 " pdb=" C04 PGV C 303 " pdb=" C06 PGV C 303 " pdb=" O05 PGV C 303 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C05 PGV B 203 " pdb=" C04 PGV B 203 " pdb=" C06 PGV B 203 " pdb=" O05 PGV B 203 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C05 PGV J 204 " pdb=" C04 PGV J 204 " pdb=" C06 PGV J 204 " pdb=" O05 PGV J 204 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2382 not shown) Planarity restraints: 2705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " -0.014 2.00e-02 2.50e+03 3.31e-02 2.47e+01 pdb=" C2C HEC C 301 " 0.090 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " -0.020 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " -0.015 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 301 " -0.011 2.00e-02 2.50e+03 3.04e-02 2.08e+01 pdb=" C2C HEC K 301 " 0.083 2.00e-02 2.50e+03 pdb=" C3C HEC K 301 " -0.003 2.00e-02 2.50e+03 pdb=" C4C HEC K 301 " -0.001 2.00e-02 2.50e+03 pdb=" CAC HEC K 301 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 301 " -0.016 2.00e-02 2.50e+03 pdb=" CHD HEC K 301 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC K 301 " -0.025 2.00e-02 2.50e+03 pdb=" NC HEC K 301 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 86 " -0.052 5.00e-02 4.00e+02 7.93e-02 1.00e+01 pdb=" N PRO C 87 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.043 5.00e-02 4.00e+02 ... (remaining 2702 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 268 2.66 - 3.22: 14736 3.22 - 3.78: 25345 3.78 - 4.34: 35380 4.34 - 4.90: 58137 Nonbonded interactions: 133866 Sorted by model distance: nonbonded pdb=" NE2 HIS I 93 " pdb="FE HEM I 303 " model vdw 2.106 3.080 nonbonded pdb=" NE2 HIS I 209 " pdb="FE HEM I 304 " model vdw 2.170 3.080 nonbonded pdb=" OH TYR I 65 " pdb=" O LEU I 145 " model vdw 2.201 3.040 nonbonded pdb=" NE2 HIS A 209 " pdb="FE HEM A 303 " model vdw 2.210 3.080 nonbonded pdb=" O PHE I 59 " pdb=" OG1 THR I 62 " model vdw 2.211 3.040 ... (remaining 133861 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' and (resid 3 through 301 or resid 303)) selection = (chain 'I' and (resid 3 through 301 or resid 303)) } ncs_group { reference = (chain 'B' and (resid 2 through 159 or (resid 202 and (name C01 or name C02 or n \ ame C03 or name C04 or name C05 or name C06 or name C1 or name C10 or name C11 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O \ 03 or name O04 or name O05 or name O06 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or resid 203)) selection = (chain 'J' and (resid 2 through 159 or (resid 203 and (name C01 or name C02 or n \ ame C03 or name C04 or name C05 or name C06 or name C1 or name C10 or name C11 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O \ 03 or name O04 or name O05 or name O06 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or (resid 204 and (name C01 or name C02 or name C03 or name \ C04 or name C05 or name C06 or name C1 or name C10 or name C11 or name C19 or na \ me C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O \ 05 or name O06 or name O11 or name O12 or name O13 or name O14 or name P )))) } ncs_group { reference = (chain 'C' and resid 1 through 301) selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = (chain 'E' and resid 1 through 32) selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 34) selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.170 Find NCS groups from input model: 0.330 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.011 0.715 16053 Z= 0.343 Angle : 0.987 37.125 21896 Z= 0.404 Chirality : 0.046 0.237 2385 Planarity : 0.005 0.101 2705 Dihedral : 15.106 164.559 5736 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1873 helix: 0.96 (0.17), residues: 930 sheet: -1.75 (0.37), residues: 182 loop : -1.49 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.012 0.001 TYR B 80 PHE 0.044 0.002 PHE A 138 TRP 0.041 0.001 TRP L 190 HIS 0.009 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.28 (16032) covalent geometry : angle 0.93569 / 0.40 (21888) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 0.78652 / 0.46 ( 2) hydrogen bonds : bond 0.12961 / 8.78 ( 793) hydrogen bonds : angle 6.11020 / 4.30 ( 2298) metal coordination : bond 0.31854 / 18.24 ( 8) metal coordination : angle 18.95896 / 11.47 ( 6) Misc. bond : bond 0.19364 / 10.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.527 Fit side-chains REVERT: A 103 MET cc_start: 0.8118 (mmp) cc_final: 0.7321 (mmt) REVERT: B 153 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7941 (pttt) REVERT: K 138 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6841 (pttm) REVERT: P 14 LEU cc_start: 0.8789 (tp) cc_final: 0.8447 (tt) REVERT: P 21 MET cc_start: 0.8176 (mmp) cc_final: 0.7906 (mmp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1167 time to fit residues: 40.1184 Evaluate side-chains 209 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 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 = 0.3679 r_free = 0.3679 target = 0.151700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117745 restraints weight = 17763.237| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.24 r_work: 0.2984 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.500 16053 Z= 0.159 Angle : 0.652 15.571 21896 Z= 0.286 Chirality : 0.043 0.224 2385 Planarity : 0.005 0.060 2705 Dihedral : 13.192 144.905 2424 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.39 % Allowed : 5.80 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1873 helix: 1.36 (0.17), residues: 931 sheet: -1.40 (0.43), residues: 142 loop : -1.38 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 184 TYR 0.011 0.001 TYR C 102 PHE 0.022 0.002 PHE I 138 TRP 0.021 0.001 TRP L 190 HIS 0.007 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 (16032) covalent geometry : angle 0.64690 / 0.29 (21888) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 1.05755 / 0.62 ( 2) hydrogen bonds : bond 0.04612 / 2.98 ( 793) hydrogen bonds : angle 4.85059 / 3.42 ( 2298) metal coordination : bond 0.01874 / 1.17 ( 8) metal coordination : angle 5.04665 / 2.85 ( 6) Misc. bond : bond 0.21305 / 12.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.417 Fit side-chains REVERT: A 103 MET cc_start: 0.8664 (mmp) cc_final: 0.8119 (mmt) REVERT: B 153 LYS cc_start: 0.8447 (ptpp) cc_final: 0.7826 (pttt) REVERT: C 62 LEU cc_start: 0.8565 (mt) cc_final: 0.8252 (mt) REVERT: D 150 LYS cc_start: 0.7383 (tmtt) cc_final: 0.7156 (tmtt) REVERT: D 160 LEU cc_start: 0.7598 (mt) cc_final: 0.7390 (mt) REVERT: K 138 LYS cc_start: 0.7547 (mtmt) cc_final: 0.6887 (pttm) REVERT: P 21 MET cc_start: 0.8770 (mmp) cc_final: 0.8547 (mmp) outliers start: 6 outliers final: 3 residues processed: 217 average time/residue: 0.1129 time to fit residues: 36.6484 Evaluate side-chains 207 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 168 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114575 restraints weight = 18026.284| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.47 r_work: 0.2908 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.478 16053 Z= 0.165 Angle : 0.647 18.333 21896 Z= 0.278 Chirality : 0.043 0.191 2385 Planarity : 0.004 0.055 2705 Dihedral : 12.557 114.702 2424 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 7.47 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1873 helix: 1.41 (0.17), residues: 932 sheet: -1.56 (0.40), residues: 160 loop : -1.26 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 15 TYR 0.010 0.001 TYR G 29 PHE 0.019 0.002 PHE I 138 TRP 0.016 0.001 TRP I 153 HIS 0.007 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (16032) covalent geometry : angle 0.64185 / 0.28 (21888) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.70630 / 0.41 ( 2) hydrogen bonds : bond 0.04504 / 2.92 ( 793) hydrogen bonds : angle 4.66654 / 3.30 ( 2298) metal coordination : bond 0.01065 / 0.73 ( 8) metal coordination : angle 5.14847 / 2.79 ( 6) Misc. bond : bond 0.19873 / 11.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.597 Fit side-chains REVERT: A 8 GLU cc_start: 0.6329 (tm-30) cc_final: 0.6097 (tt0) REVERT: A 103 MET cc_start: 0.8728 (mmp) cc_final: 0.8269 (mmp) REVERT: A 138 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8150 (t80) REVERT: B 153 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7873 (pttt) REVERT: C 62 LEU cc_start: 0.8581 (mt) cc_final: 0.8249 (mt) REVERT: C 262 MET cc_start: 0.8705 (mtp) cc_final: 0.8483 (mtp) REVERT: D 160 LEU cc_start: 0.7691 (mt) cc_final: 0.7432 (mt) REVERT: D 175 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5903 (mp) REVERT: I 103 MET cc_start: 0.8757 (mmt) cc_final: 0.8138 (mmp) REVERT: K 135 ASP cc_start: 0.8397 (t0) cc_final: 0.8160 (t0) REVERT: K 138 LYS cc_start: 0.7570 (mtmt) cc_final: 0.6881 (pttm) REVERT: L 89 ASP cc_start: 0.5946 (m-30) cc_final: 0.5662 (m-30) outliers start: 14 outliers final: 7 residues processed: 219 average time/residue: 0.1071 time to fit residues: 35.3344 Evaluate side-chains 216 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 94 optimal weight: 0.0970 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 110 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.155474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123986 restraints weight = 17798.820| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.08 r_work: 0.3017 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.441 16053 Z= 0.121 Angle : 0.591 14.506 21896 Z= 0.258 Chirality : 0.042 0.185 2385 Planarity : 0.004 0.050 2705 Dihedral : 12.000 97.752 2424 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.39 % Allowed : 9.47 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1873 helix: 1.66 (0.17), residues: 932 sheet: -1.46 (0.43), residues: 136 loop : -1.14 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 15 TYR 0.009 0.001 TYR B 80 PHE 0.016 0.001 PHE A 12 TRP 0.016 0.001 TRP I 153 HIS 0.004 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16032) covalent geometry : angle 0.58525 / 0.26 (21888) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.58763 / 0.34 ( 2) hydrogen bonds : bond 0.04104 / 2.67 ( 793) hydrogen bonds : angle 4.47218 / 3.16 ( 2298) metal coordination : bond 0.00605 / 0.40 ( 8) metal coordination : angle 4.93195 / 2.62 ( 6) Misc. bond : bond 0.17774 / 9.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.438 Fit side-chains REVERT: A 103 MET cc_start: 0.8669 (mmp) cc_final: 0.8196 (mmt) REVERT: A 138 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7945 (t80) REVERT: B 130 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8100 (mmp) REVERT: B 153 LYS cc_start: 0.8411 (ptpp) cc_final: 0.7874 (pttt) REVERT: C 62 LEU cc_start: 0.8505 (mt) cc_final: 0.8219 (mt) REVERT: C 262 MET cc_start: 0.8635 (mtp) cc_final: 0.8369 (mtp) REVERT: D 175 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5905 (mp) REVERT: I 103 MET cc_start: 0.8728 (mmt) cc_final: 0.8149 (mmp) REVERT: K 135 ASP cc_start: 0.8329 (t0) cc_final: 0.8127 (t0) REVERT: K 138 LYS cc_start: 0.7570 (mtmt) cc_final: 0.6946 (pttm) REVERT: L 89 ASP cc_start: 0.5979 (m-30) cc_final: 0.5678 (m-30) outliers start: 6 outliers final: 3 residues processed: 225 average time/residue: 0.1156 time to fit residues: 39.0114 Evaluate side-chains 212 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 11 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 52 optimal weight: 10.0000 chunk 47 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124827 restraints weight = 17724.735| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.18 r_work: 0.2896 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.442 16053 Z= 0.135 Angle : 0.611 16.640 21896 Z= 0.263 Chirality : 0.042 0.165 2385 Planarity : 0.004 0.048 2705 Dihedral : 11.822 96.020 2424 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.90 % Allowed : 9.85 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1873 helix: 1.70 (0.17), residues: 932 sheet: -1.42 (0.43), residues: 136 loop : -1.09 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.010 0.001 TYR B 80 PHE 0.017 0.001 PHE A 12 TRP 0.016 0.001 TRP I 153 HIS 0.005 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (16032) covalent geometry : angle 0.60685 / 0.26 (21888) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 0.57152 / 0.33 ( 2) hydrogen bonds : bond 0.04175 / 2.71 ( 793) hydrogen bonds : angle 4.42812 / 3.13 ( 2298) metal coordination : bond 0.00666 / 0.46 ( 8) metal coordination : angle 4.43097 / 2.31 ( 6) Misc. bond : bond 0.18061 / 9.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.340 Fit side-chains REVERT: A 103 MET cc_start: 0.8740 (mmp) cc_final: 0.8165 (mmt) REVERT: A 138 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.7979 (t80) REVERT: B 15 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7241 (ttp-110) REVERT: B 130 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8681 (mmp) REVERT: B 153 LYS cc_start: 0.8374 (ptpp) cc_final: 0.7803 (pttt) REVERT: C 62 LEU cc_start: 0.8532 (mt) cc_final: 0.8241 (mt) REVERT: C 123 GLN cc_start: 0.7827 (pm20) cc_final: 0.7529 (pt0) REVERT: D 175 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5783 (mp) REVERT: K 135 ASP cc_start: 0.8340 (t0) cc_final: 0.8054 (t0) REVERT: K 138 LYS cc_start: 0.7608 (mtmt) cc_final: 0.6932 (pttm) REVERT: M 11 TYR cc_start: 0.7376 (t80) cc_final: 0.7097 (t80) outliers start: 14 outliers final: 7 residues processed: 221 average time/residue: 0.1155 time to fit residues: 37.8669 Evaluate side-chains 214 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 161 optimal weight: 0.0570 chunk 47 optimal weight: 0.1980 chunk 154 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.156897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124056 restraints weight = 17690.225| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.21 r_work: 0.2923 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.424 16053 Z= 0.117 Angle : 0.585 14.556 21896 Z= 0.254 Chirality : 0.041 0.166 2385 Planarity : 0.004 0.045 2705 Dihedral : 11.499 91.615 2424 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.90 % Allowed : 10.62 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1873 helix: 1.82 (0.17), residues: 932 sheet: -1.20 (0.40), residues: 164 loop : -1.13 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.009 0.001 TYR B 80 PHE 0.015 0.001 PHE A 12 TRP 0.015 0.001 TRP I 153 HIS 0.003 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 (16032) covalent geometry : angle 0.58050 / 0.25 (21888) SS BOND : bond 0.00046 / 0.02 ( 1) SS BOND : angle 0.52548 / 0.31 ( 2) hydrogen bonds : bond 0.04000 / 2.60 ( 793) hydrogen bonds : angle 4.33051 / 3.07 ( 2298) metal coordination : bond 0.00414 / 0.28 ( 8) metal coordination : angle 4.40281 / 2.32 ( 6) Misc. bond : bond 0.16966 / 9.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.478 Fit side-chains REVERT: A 103 MET cc_start: 0.8672 (mmp) cc_final: 0.8436 (mmp) REVERT: A 138 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7922 (t80) REVERT: B 15 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7253 (ttp-110) REVERT: B 130 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8602 (mmp) REVERT: B 153 LYS cc_start: 0.8383 (ptpp) cc_final: 0.7785 (pttt) REVERT: C 62 LEU cc_start: 0.8578 (mt) cc_final: 0.8270 (mt) REVERT: D 92 LEU cc_start: 0.7875 (pp) cc_final: 0.7498 (pp) REVERT: D 160 LEU cc_start: 0.7489 (mt) cc_final: 0.7274 (mt) REVERT: D 175 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5776 (mp) REVERT: I 103 MET cc_start: 0.8736 (mmt) cc_final: 0.8176 (mmp) REVERT: K 138 LYS cc_start: 0.7613 (mtmt) cc_final: 0.6963 (pttm) REVERT: L 148 GLU cc_start: 0.8177 (pt0) cc_final: 0.7638 (pt0) REVERT: M 11 TYR cc_start: 0.7319 (t80) cc_final: 0.6996 (t80) outliers start: 14 outliers final: 8 residues processed: 218 average time/residue: 0.1168 time to fit residues: 38.2529 Evaluate side-chains 214 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121876 restraints weight = 17663.466| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.13 r_work: 0.2904 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.444 16053 Z= 0.157 Angle : 0.629 17.510 21896 Z= 0.269 Chirality : 0.043 0.164 2385 Planarity : 0.004 0.045 2705 Dihedral : 11.550 93.058 2424 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.97 % Allowed : 10.82 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1873 helix: 1.71 (0.17), residues: 932 sheet: -1.19 (0.42), residues: 154 loop : -1.10 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.011 0.001 TYR B 80 PHE 0.015 0.001 PHE A 12 TRP 0.015 0.001 TRP I 153 HIS 0.005 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (16032) covalent geometry : angle 0.62420 / 0.27 (21888) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.64432 / 0.37 ( 2) hydrogen bonds : bond 0.04270 / 2.77 ( 793) hydrogen bonds : angle 4.40534 / 3.12 ( 2298) metal coordination : bond 0.00820 / 0.54 ( 8) metal coordination : angle 4.50376 / 2.41 ( 6) Misc. bond : bond 0.18462 / 10.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.509 Fit side-chains REVERT: A 103 MET cc_start: 0.8669 (mmp) cc_final: 0.8029 (mmp) REVERT: A 138 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8050 (t80) REVERT: B 15 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7175 (ttp-110) REVERT: B 130 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8675 (mmp) REVERT: B 153 LYS cc_start: 0.8388 (ptpp) cc_final: 0.7781 (pttt) REVERT: C 123 GLN cc_start: 0.7871 (pm20) cc_final: 0.7542 (pt0) REVERT: D 160 LEU cc_start: 0.7397 (mt) cc_final: 0.7187 (mt) REVERT: K 19 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8431 (ttt-90) REVERT: K 135 ASP cc_start: 0.8413 (t0) cc_final: 0.8037 (t0) REVERT: K 138 LYS cc_start: 0.7665 (mtmt) cc_final: 0.6930 (pttm) outliers start: 15 outliers final: 10 residues processed: 217 average time/residue: 0.1110 time to fit residues: 36.3255 Evaluate side-chains 216 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 33 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN ** K 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118175 restraints weight = 17762.958| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.15 r_work: 0.2907 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.427 16053 Z= 0.131 Angle : 0.606 15.591 21896 Z= 0.262 Chirality : 0.042 0.166 2385 Planarity : 0.004 0.043 2705 Dihedral : 11.363 91.070 2424 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.84 % Allowed : 11.01 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1873 helix: 1.79 (0.17), residues: 932 sheet: -1.16 (0.42), residues: 154 loop : -1.05 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.010 0.001 TYR B 80 PHE 0.015 0.001 PHE M 15 TRP 0.015 0.001 TRP I 153 HIS 0.004 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (16032) covalent geometry : angle 0.60214 / 0.26 (21888) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.60373 / 0.35 ( 2) hydrogen bonds : bond 0.04108 / 2.67 ( 793) hydrogen bonds : angle 4.33899 / 3.07 ( 2298) metal coordination : bond 0.00509 / 0.33 ( 8) metal coordination : angle 4.21569 / 2.26 ( 6) Misc. bond : bond 0.17652 / 9.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.567 Fit side-chains REVERT: A 138 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 15 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7187 (ttp-110) REVERT: B 130 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8615 (mmp) REVERT: B 153 LYS cc_start: 0.8388 (ptpp) cc_final: 0.7786 (pttt) REVERT: I 8 GLU cc_start: 0.6334 (pp20) cc_final: 0.6065 (pm20) REVERT: K 19 ARG cc_start: 0.8735 (ttt180) cc_final: 0.8439 (ttt-90) REVERT: K 138 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7099 (pttm) REVERT: L 148 GLU cc_start: 0.8087 (pt0) cc_final: 0.7559 (pt0) outliers start: 13 outliers final: 9 residues processed: 210 average time/residue: 0.1109 time to fit residues: 35.2247 Evaluate side-chains 212 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** 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 = 0.3706 r_free = 0.3706 target = 0.153696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120036 restraints weight = 17779.959| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.13 r_work: 0.2907 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.430 16053 Z= 0.144 Angle : 0.620 16.500 21896 Z= 0.267 Chirality : 0.042 0.164 2385 Planarity : 0.004 0.043 2705 Dihedral : 11.318 90.674 2424 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 11.08 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1873 helix: 1.76 (0.17), residues: 932 sheet: -1.18 (0.42), residues: 154 loop : -1.02 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.011 0.001 TYR B 80 PHE 0.017 0.001 PHE M 15 TRP 0.015 0.001 TRP I 153 HIS 0.005 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (16032) covalent geometry : angle 0.61664 / 0.27 (21888) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.62429 / 0.36 ( 2) hydrogen bonds : bond 0.04194 / 2.72 ( 793) hydrogen bonds : angle 4.35483 / 3.08 ( 2298) metal coordination : bond 0.00463 / 0.29 ( 8) metal coordination : angle 3.88172 / 2.11 ( 6) Misc. bond : bond 0.18065 / 9.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.462 Fit side-chains REVERT: A 103 MET cc_start: 0.8486 (mmp) cc_final: 0.8230 (mmp) REVERT: A 138 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8065 (t80) REVERT: B 130 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8636 (mmp) REVERT: B 153 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7777 (pttt) REVERT: C 62 LEU cc_start: 0.8609 (mt) cc_final: 0.8342 (mp) REVERT: C 123 GLN cc_start: 0.7748 (pm20) cc_final: 0.7479 (pt0) REVERT: I 8 GLU cc_start: 0.6107 (pp20) cc_final: 0.5851 (pm20) REVERT: K 19 ARG cc_start: 0.8717 (ttt180) cc_final: 0.8402 (ttt-90) REVERT: K 138 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7066 (pttm) REVERT: L 148 GLU cc_start: 0.8086 (pt0) cc_final: 0.7549 (pt0) outliers start: 14 outliers final: 10 residues processed: 212 average time/residue: 0.1240 time to fit residues: 39.2171 Evaluate side-chains 213 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.156029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122340 restraints weight = 17623.557| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.09 r_work: 0.2854 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.420 16053 Z= 0.125 Angle : 0.606 15.336 21896 Z= 0.262 Chirality : 0.042 0.163 2385 Planarity : 0.004 0.042 2705 Dihedral : 11.167 87.562 2424 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 11.20 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1873 helix: 1.83 (0.17), residues: 932 sheet: -1.30 (0.38), residues: 188 loop : -0.99 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.012 0.001 TYR B 80 PHE 0.016 0.001 PHE M 15 TRP 0.015 0.001 TRP I 153 HIS 0.003 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (16032) covalent geometry : angle 0.60184 / 0.26 (21888) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.60248 / 0.35 ( 2) hydrogen bonds : bond 0.04067 / 2.64 ( 793) hydrogen bonds : angle 4.29474 / 3.04 ( 2298) metal coordination : bond 0.00413 / 0.26 ( 8) metal coordination : angle 4.08069 / 2.18 ( 6) Misc. bond : bond 0.17303 / 9.45 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.629 Fit side-chains REVERT: A 138 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.7922 (t80) REVERT: B 110 LEU cc_start: 0.8589 (mp) cc_final: 0.8354 (mp) REVERT: B 130 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8677 (mmp) REVERT: B 153 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7714 (pttt) REVERT: C 62 LEU cc_start: 0.8598 (mt) cc_final: 0.8315 (mp) REVERT: I 8 GLU cc_start: 0.6218 (pp20) cc_final: 0.5951 (pm20) REVERT: K 19 ARG cc_start: 0.8745 (ttt180) cc_final: 0.8449 (ttt-90) REVERT: K 138 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7020 (pttm) REVERT: L 148 GLU cc_start: 0.8158 (pt0) cc_final: 0.7577 (pt0) outliers start: 14 outliers final: 10 residues processed: 211 average time/residue: 0.1302 time to fit residues: 41.2815 Evaluate side-chains 213 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 102 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.0020 chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.151779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118807 restraints weight = 17756.214| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.16 r_work: 0.2892 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.437 16053 Z= 0.160 Angle : 0.644 17.158 21896 Z= 0.278 Chirality : 0.043 0.165 2385 Planarity : 0.004 0.043 2705 Dihedral : 11.214 89.691 2424 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.77 % Allowed : 11.40 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1873 helix: 1.69 (0.17), residues: 934 sheet: -1.21 (0.42), residues: 154 loop : -0.98 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.013 0.001 TYR B 80 PHE 0.017 0.001 PHE E 15 TRP 0.015 0.001 TRP I 153 HIS 0.006 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (16032) covalent geometry : angle 0.64018 / 0.28 (21888) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.67042 / 0.39 ( 2) hydrogen bonds : bond 0.04291 / 2.78 ( 793) hydrogen bonds : angle 4.37624 / 3.10 ( 2298) metal coordination : bond 0.00749 / 0.46 ( 8) metal coordination : angle 4.16298 / 2.25 ( 6) Misc. bond : bond 0.18569 / 10.20 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3764.43 seconds wall clock time: 65 minutes 9.03 seconds (3909.03 seconds total)