Starting phenix.real_space_refine on Mon Mar 11 10:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/03_2024/8ucd_42124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/03_2024/8ucd_42124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/03_2024/8ucd_42124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/03_2024/8ucd_42124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/03_2024/8ucd_42124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/03_2024/8ucd_42124_updated.pdb" } resolution = 3.0 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= 0.025 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 9 5.49 5 S 22 5.16 5 C 5425 2.51 5 N 1252 2.21 5 O 1347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8058 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1980 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1966 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 13, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1969 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'FAD': 1, 'HEM': 1, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FAD:plan-1': 1, 'FAD:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'FAD': 1, 'HEM': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'FAD:plan-1': 1, 'FAD:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'FAD': 1, 'HEM': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'FAD:plan-1': 1, 'FAD:plan-3': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 4.81, per 1000 atoms: 0.60 Number of scatterers: 8058 At special positions: 0 Unit cell: (104.92, 88.58, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 22 16.00 P 9 15.00 O 1347 8.00 N 1252 7.00 C 5425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 144 " - pdb=" SG CYS L 208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 6 sheets defined 58.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 69 through 93 removed outlier: 3.635A pdb=" N HIS A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 73 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 3.525A pdb=" N ILE A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 78 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 80 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 90 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 141 removed outlier: 4.490A pdb=" N LEU A 118 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Proline residue: A 119 - end of helix removed outlier: 3.852A pdb=" N LEU A 131 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Proline residue: A 132 - end of helix removed outlier: 3.546A pdb=" N ALA A 137 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 161 through 181 removed outlier: 3.949A pdb=" N SER A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 Processing helix chain 'A' and resid 210 through 237 removed outlier: 4.209A pdb=" N SER A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 4.215A pdb=" N SER A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 272 removed outlier: 3.732A pdb=" N LEU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'B' and resid 73 through 93 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 118 through 140 removed outlier: 4.094A pdb=" N TYR B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 152 through 181 removed outlier: 4.146A pdb=" N THR B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 201 Processing helix chain 'B' and resid 210 through 237 removed outlier: 3.874A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.626A pdb=" N ASP B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 244' Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.714A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'C' and resid 69 through 93 removed outlier: 3.591A pdb=" N HIS C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU C 73 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 4.028A pdb=" N ILE C 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 83 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 84 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 87 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 90 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 118 through 141 removed outlier: 3.511A pdb=" N VAL C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Proline residue: C 132 - end of helix removed outlier: 3.526A pdb=" N ILE C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 184 removed outlier: 3.942A pdb=" N THR C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 182 " --> pdb=" O TYR C 178 " (cutoff:3.500A) Proline residue: C 183 - end of helix Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.530A pdb=" N GLN C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 237 removed outlier: 3.803A pdb=" N TYR C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL C 220 " --> pdb=" O MET C 216 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.689A pdb=" N ASP C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 244' Processing helix chain 'C' and resid 248 through 272 removed outlier: 3.616A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 296 through 309 Processing sheet with id= A, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= B, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.472A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 97 through 102 Processing sheet with id= D, first strand: chain 'L' and resid 131 through 133 removed outlier: 7.606A pdb=" N LYS L 223 " --> pdb=" O LEU L 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'L' and resid 140 through 144 removed outlier: 3.832A pdb=" N TYR L 191 " --> pdb=" O CYS L 144 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 205 through 209 removed outlier: 5.965A pdb=" N GLN L 157 " --> pdb=" O LEU L 166 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU L 166 " --> pdb=" O GLN L 157 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1059 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: 2.13 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2315 1.36 - 1.53: 5494 1.53 - 1.71: 463 1.71 - 1.88: 40 1.88 - 2.06: 12 Bond restraints: 8324 Sorted by residual: bond pdb=" C25 LBN A 403 " pdb=" O5 LBN A 403 " ideal model delta sigma weight residual 1.326 1.434 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C25 LBN B 401 " pdb=" O5 LBN B 401 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C25 LBN A 401 " pdb=" O5 LBN A 401 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C41 LBN A 403 " pdb=" C42 LBN A 403 " ideal model delta sigma weight residual 1.497 1.573 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C41 LBN B 401 " pdb=" C42 LBN B 401 " ideal model delta sigma weight residual 1.497 1.573 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 8319 not shown) Histogram of bond angle deviations from ideal: 89.30 - 106.13: 229 106.13 - 122.97: 10477 122.97 - 139.80: 683 139.80 - 156.63: 0 156.63 - 173.46: 6 Bond angle restraints: 11395 Sorted by residual: angle pdb=" O1 LBN A 401 " pdb=" P1 LBN A 401 " pdb=" O2 LBN A 401 " ideal model delta sigma weight residual 93.45 109.94 -16.49 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O1 LBN B 401 " pdb=" P1 LBN B 401 " pdb=" O2 LBN B 401 " ideal model delta sigma weight residual 93.45 109.71 -16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" O1 LBN A 403 " pdb=" P1 LBN A 403 " pdb=" O2 LBN A 403 " ideal model delta sigma weight residual 93.45 109.40 -15.95 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O3 LBN A 401 " pdb=" P1 LBN A 401 " pdb=" O4 LBN A 401 " ideal model delta sigma weight residual 119.36 109.27 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O3 LBN A 403 " pdb=" P1 LBN A 403 " pdb=" O4 LBN A 403 " ideal model delta sigma weight residual 119.36 109.45 9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 11390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 4663 35.85 - 71.70: 119 71.70 - 107.55: 11 107.55 - 143.39: 7 143.39 - 179.24: 4 Dihedral angle restraints: 4804 sinusoidal: 2023 harmonic: 2781 Sorted by residual: dihedral pdb=" C40 LBN A 403 " pdb=" C41 LBN A 403 " pdb=" C42 LBN A 403 " pdb=" C5 LBN A 403 " ideal model delta sinusoidal sigma weight residual 117.80 -62.96 -179.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' FAD C 401 " pdb=" O3P FAD C 401 " pdb=" P FAD C 401 " pdb=" PA FAD C 401 " ideal model delta sinusoidal sigma weight residual 298.23 131.51 166.72 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" N1 LBN A 403 " pdb=" C6 LBN A 403 " pdb=" C9 LBN A 403 " pdb=" O2 LBN A 403 " ideal model delta sinusoidal sigma weight residual 71.48 -131.23 -157.29 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 857 0.036 - 0.072: 298 0.072 - 0.108: 69 0.108 - 0.144: 24 0.144 - 0.180: 3 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C2 LBN A 401 " pdb=" C1 LBN A 401 " pdb=" C3 LBN A 401 " pdb=" O7 LBN A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C2 LBN B 401 " pdb=" C1 LBN B 401 " pdb=" C3 LBN B 401 " pdb=" O7 LBN B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.52 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" C2 LBN A 403 " pdb=" C1 LBN A 403 " pdb=" C3 LBN A 403 " pdb=" O7 LBN A 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.52 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1248 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 247 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C TRP C 247 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP C 247 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG C 248 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 109 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO C 110 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 135 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO L 136 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO L 136 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 136 " -0.021 5.00e-02 4.00e+02 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 187 2.72 - 3.26: 7572 3.26 - 3.81: 12335 3.81 - 4.35: 15044 4.35 - 4.90: 26823 Nonbonded interactions: 61961 Sorted by model distance: nonbonded pdb=" O2' FAD A 402 " pdb=" O4' FAD A 402 " model vdw 2.171 2.440 nonbonded pdb=" NE1 TRP B 71 " pdb=" O4 LBN B 401 " model vdw 2.313 2.520 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.319 2.440 nonbonded pdb=" NE2 GLN B 70 " pdb=" O3 LBN B 401 " model vdw 2.326 2.520 nonbonded pdb=" ND2 ASN B 115 " pdb=" OH TYR B 182 " model vdw 2.346 2.520 ... (remaining 61956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 141 or resid 150 through 310)) selection = (chain 'B' and (resid 67 through 309 or (resid 310 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'C' and (resid 67 through 141 or resid 150 through 309 or (resid 310 and \ (name N or name CA or name C or name O or name CB )))) } 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: 7.000 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: 0.020 Extract box with map and model: 19.610 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 25.320 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 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:18.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.007 0.108 8324 Z= 0.450 Angle : 0.862 16.493 11395 Z= 0.356 Chirality : 0.041 0.180 1251 Planarity : 0.004 0.040 1317 Dihedral : 17.938 179.242 2998 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % 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: 0.96 (0.30), residues: 923 helix: 1.57 (0.24), residues: 578 sheet: 1.00 (0.52), residues: 111 loop : -1.95 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 285 HIS 0.004 0.001 HIS A 268 PHE 0.011 0.001 PHE L 156 TYR 0.013 0.001 TYR A 219 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.843 Fit side-chains REVERT: B 198 GLN cc_start: 0.7657 (tt0) cc_final: 0.7306 (tt0) REVERT: L 134 LEU cc_start: 0.7762 (tp) cc_final: 0.7504 (tp) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 1.3710 time to fit residues: 117.9667 Evaluate side-chains 60 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 202 GLN A 251 HIS B 202 GLN B 254 GLN C 254 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8324 Z= 0.206 Angle : 0.638 11.950 11395 Z= 0.289 Chirality : 0.041 0.150 1251 Planarity : 0.005 0.043 1317 Dihedral : 17.692 171.139 1260 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.09 % Allowed : 9.07 % Favored : 89.84 % 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: 0.86 (0.30), residues: 923 helix: 1.49 (0.24), residues: 575 sheet: 0.74 (0.51), residues: 117 loop : -1.88 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 285 HIS 0.007 0.001 HIS A 268 PHE 0.013 0.001 PHE L 156 TYR 0.035 0.002 TYR B 219 ARG 0.001 0.000 ARG L 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.828 Fit side-chains REVERT: B 198 GLN cc_start: 0.7806 (tt0) cc_final: 0.7457 (tt0) REVERT: B 206 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7992 (t70) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 1.2824 time to fit residues: 90.2243 Evaluate side-chains 63 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8324 Z= 0.206 Angle : 0.618 11.885 11395 Z= 0.280 Chirality : 0.040 0.142 1251 Planarity : 0.004 0.041 1317 Dihedral : 16.741 179.597 1260 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.81 % Allowed : 11.85 % Favored : 86.34 % 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: 0.79 (0.29), residues: 923 helix: 1.42 (0.23), residues: 574 sheet: 0.85 (0.51), residues: 112 loop : -1.89 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 285 HIS 0.007 0.001 HIS A 268 PHE 0.013 0.001 PHE L 156 TYR 0.026 0.001 TYR A 219 ARG 0.001 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.935 Fit side-chains REVERT: A 93 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: B 198 GLN cc_start: 0.7856 (tt0) cc_final: 0.7485 (tt0) outliers start: 15 outliers final: 4 residues processed: 62 average time/residue: 1.2877 time to fit residues: 85.2450 Evaluate side-chains 61 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 216 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8324 Z= 0.216 Angle : 0.623 12.129 11395 Z= 0.283 Chirality : 0.041 0.152 1251 Planarity : 0.004 0.040 1317 Dihedral : 16.327 173.945 1260 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.42 % Allowed : 12.70 % Favored : 84.89 % 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: 0.72 (0.29), residues: 923 helix: 1.36 (0.23), residues: 574 sheet: 0.88 (0.51), residues: 113 loop : -1.96 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 285 HIS 0.007 0.001 HIS A 268 PHE 0.013 0.001 PHE L 156 TYR 0.027 0.002 TYR B 219 ARG 0.002 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.954 Fit side-chains REVERT: B 198 GLN cc_start: 0.7858 (tt0) cc_final: 0.7478 (tt0) REVERT: B 206 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7911 (t70) outliers start: 20 outliers final: 9 residues processed: 71 average time/residue: 1.2977 time to fit residues: 98.1565 Evaluate side-chains 70 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 216 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8324 Z= 0.261 Angle : 0.671 13.248 11395 Z= 0.304 Chirality : 0.042 0.153 1251 Planarity : 0.005 0.041 1317 Dihedral : 16.066 170.937 1260 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.54 % Allowed : 13.30 % Favored : 84.16 % 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: 0.53 (0.29), residues: 923 helix: 1.20 (0.23), residues: 577 sheet: 0.60 (0.50), residues: 118 loop : -1.95 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 285 HIS 0.008 0.002 HIS A 268 PHE 0.013 0.001 PHE L 156 TYR 0.027 0.002 TYR A 219 ARG 0.002 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.929 Fit side-chains REVERT: A 191 LYS cc_start: 0.7932 (mttt) cc_final: 0.7321 (mtpt) REVERT: B 198 GLN cc_start: 0.7928 (tt0) cc_final: 0.7541 (tt0) REVERT: B 206 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7943 (t70) REVERT: C 120 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7186 (ttt) outliers start: 21 outliers final: 9 residues processed: 71 average time/residue: 1.3207 time to fit residues: 100.2845 Evaluate side-chains 71 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 216 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8324 Z= 0.263 Angle : 0.668 13.182 11395 Z= 0.302 Chirality : 0.042 0.149 1251 Planarity : 0.005 0.058 1317 Dihedral : 15.805 167.223 1260 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.14 % Allowed : 13.66 % Favored : 83.19 % 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: 0.55 (0.29), residues: 923 helix: 1.20 (0.23), residues: 570 sheet: 0.65 (0.51), residues: 117 loop : -1.80 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.008 0.002 HIS A 268 PHE 0.013 0.001 PHE B 170 TYR 0.026 0.002 TYR A 219 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 0.972 Fit side-chains REVERT: A 93 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 104 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7236 (pp30) REVERT: A 191 LYS cc_start: 0.7940 (mttt) cc_final: 0.7318 (mtpt) REVERT: B 198 GLN cc_start: 0.7921 (tt0) cc_final: 0.7538 (tt0) REVERT: B 206 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7970 (t70) REVERT: H 113 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8106 (pt0) outliers start: 26 outliers final: 9 residues processed: 76 average time/residue: 1.3218 time to fit residues: 106.8754 Evaluate side-chains 74 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain L residue 202 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8324 Z= 0.212 Angle : 0.625 12.222 11395 Z= 0.282 Chirality : 0.041 0.152 1251 Planarity : 0.005 0.050 1317 Dihedral : 15.446 169.819 1260 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.30 % Allowed : 15.48 % Favored : 82.22 % 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: 0.72 (0.29), residues: 923 helix: 1.34 (0.24), residues: 571 sheet: 0.72 (0.50), residues: 118 loop : -1.79 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 PHE 0.011 0.001 PHE L 156 TYR 0.025 0.001 TYR A 219 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.851 Fit side-chains REVERT: A 91 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 93 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: A 104 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: A 191 LYS cc_start: 0.7886 (mttt) cc_final: 0.7260 (mtpt) REVERT: B 198 GLN cc_start: 0.7891 (tt0) cc_final: 0.7564 (tt0) REVERT: H 113 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8120 (pt0) outliers start: 19 outliers final: 11 residues processed: 72 average time/residue: 1.2497 time to fit residues: 95.7745 Evaluate side-chains 75 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8324 Z= 0.253 Angle : 0.660 13.130 11395 Z= 0.298 Chirality : 0.042 0.152 1251 Planarity : 0.005 0.044 1317 Dihedral : 15.424 171.257 1260 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.66 % Allowed : 15.72 % Favored : 81.62 % 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: 0.60 (0.29), residues: 923 helix: 1.23 (0.23), residues: 571 sheet: 0.65 (0.51), residues: 118 loop : -1.79 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.008 0.002 HIS A 268 PHE 0.013 0.001 PHE B 170 TYR 0.026 0.002 TYR A 219 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.822 Fit side-chains REVERT: A 104 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7268 (pp30) REVERT: A 120 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7043 (ttp) REVERT: A 191 LYS cc_start: 0.7913 (mttt) cc_final: 0.7288 (mtpt) REVERT: B 198 GLN cc_start: 0.7920 (tt0) cc_final: 0.7602 (tt0) REVERT: H 113 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8126 (pt0) outliers start: 22 outliers final: 13 residues processed: 75 average time/residue: 1.2870 time to fit residues: 103.1186 Evaluate side-chains 77 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.0000 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8324 Z= 0.206 Angle : 0.621 12.197 11395 Z= 0.280 Chirality : 0.041 0.148 1251 Planarity : 0.005 0.045 1317 Dihedral : 15.243 175.625 1260 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.90 % Allowed : 15.72 % Favored : 81.38 % 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: 0.74 (0.29), residues: 923 helix: 1.36 (0.24), residues: 571 sheet: 0.78 (0.50), residues: 117 loop : -1.81 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 PHE 0.011 0.001 PHE B 170 TYR 0.025 0.001 TYR A 219 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 0.909 Fit side-chains REVERT: A 93 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 104 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7222 (pp30) REVERT: A 120 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7012 (ttp) REVERT: A 191 LYS cc_start: 0.7883 (mttt) cc_final: 0.7261 (mtpt) REVERT: B 198 GLN cc_start: 0.7867 (tt0) cc_final: 0.7570 (tt0) REVERT: B 206 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7916 (t70) REVERT: C 120 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7074 (ttt) REVERT: C 247 TRP cc_start: 0.5766 (t60) cc_final: 0.5446 (t60) REVERT: H 113 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8107 (pt0) outliers start: 24 outliers final: 15 residues processed: 75 average time/residue: 1.2265 time to fit residues: 98.2150 Evaluate side-chains 84 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain L residue 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0570 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.0020 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8324 Z= 0.145 Angle : 0.559 9.807 11395 Z= 0.253 Chirality : 0.039 0.145 1251 Planarity : 0.004 0.042 1317 Dihedral : 14.794 175.940 1260 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.06 % Allowed : 16.44 % Favored : 81.50 % 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: 1.06 (0.30), residues: 923 helix: 1.64 (0.24), residues: 570 sheet: 0.84 (0.51), residues: 118 loop : -1.73 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 274 HIS 0.005 0.001 HIS A 268 PHE 0.009 0.001 PHE L 156 TYR 0.023 0.001 TYR B 219 ARG 0.001 0.000 ARG C 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.849 Fit side-chains REVERT: A 93 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7585 (mm-30) REVERT: A 104 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7187 (pp30) REVERT: B 198 GLN cc_start: 0.7724 (tt0) cc_final: 0.7429 (tt0) REVERT: C 247 TRP cc_start: 0.5798 (t60) cc_final: 0.5467 (t60) outliers start: 17 outliers final: 9 residues processed: 76 average time/residue: 1.1538 time to fit residues: 93.7575 Evaluate side-chains 74 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 52 optimal weight: 0.0570 overall best weight: 0.1694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116112 restraints weight = 9677.262| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.50 r_work: 0.3147 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8324 Z= 0.142 Angle : 0.536 8.967 11395 Z= 0.244 Chirality : 0.039 0.146 1251 Planarity : 0.004 0.043 1317 Dihedral : 14.399 164.305 1260 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.57 % Allowed : 17.05 % Favored : 81.38 % 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: 1.29 (0.30), residues: 923 helix: 1.81 (0.24), residues: 572 sheet: 0.92 (0.51), residues: 118 loop : -1.65 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 274 HIS 0.005 0.001 HIS A 268 PHE 0.009 0.001 PHE L 156 TYR 0.023 0.001 TYR B 219 ARG 0.001 0.000 ARG B 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.61 seconds wall clock time: 52 minutes 36.50 seconds (3156.50 seconds total)