Starting phenix.real_space_refine on Fri Dec 8 10:01:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/12_2023/8ucd_42124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/12_2023/8ucd_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_42124/12_2023/8ucd_42124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/12_2023/8ucd_42124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/12_2023/8ucd_42124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucd_42124/12_2023/8ucd_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-1.21rc1-5172/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: 4.98, per 1000 atoms: 0.62 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 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: 1.80 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: 2.20 Time building geometry restraints manager: 3.49 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: 10.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 20.230 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.550 Find NCS groups from input model: 0.430 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.670 ------------------------------------------------------------------------------- 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 : 0.799 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 1.2952 time to fit residues: 111.4718 Evaluate side-chains 61 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2596 ------------------------------------------------------------------------------- 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: 0.0970 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 254 GLN C 254 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8324 Z= 0.185 Angle : 0.617 11.170 11395 Z= 0.279 Chirality : 0.040 0.145 1251 Planarity : 0.004 0.041 1317 Dihedral : 17.598 170.451 1260 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.21 % Allowed : 9.31 % Favored : 89.48 % 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: 0.92 (0.30), residues: 923 helix: 1.53 (0.24), residues: 576 sheet: 0.76 (0.51), residues: 117 loop : -1.88 (0.38), residues: 230 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 0.012 0.001 PHE L 156 TYR 0.035 0.001 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 74 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.936 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 1.2934 time to fit residues: 92.4388 Evaluate side-chains 63 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.0654 time to fit residues: 2.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.1280 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= 0.198 Angle : 0.615 11.782 11395 Z= 0.278 Chirality : 0.040 0.142 1251 Planarity : 0.004 0.041 1317 Dihedral : 16.529 179.320 1260 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.06 % Allowed : 11.49 % Favored : 86.46 % 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: 0.83 (0.29), residues: 923 helix: 1.46 (0.24), residues: 574 sheet: 0.82 (0.51), residues: 112 loop : -1.89 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 285 HIS 0.007 0.001 HIS A 268 PHE 0.012 0.001 PHE L 156 TYR 0.027 0.002 TYR B 219 ARG 0.001 0.000 ARG L 145 *********************** 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 76 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.936 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 67 average time/residue: 1.3059 time to fit residues: 93.4182 Evaluate side-chains 62 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1214 time to fit residues: 1.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8324 Z= 0.182 Angle : 0.594 11.473 11395 Z= 0.268 Chirality : 0.040 0.149 1251 Planarity : 0.004 0.038 1317 Dihedral : 16.110 175.098 1260 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.57 % Allowed : 13.18 % Favored : 85.25 % 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: 0.89 (0.29), residues: 923 helix: 1.50 (0.24), residues: 575 sheet: 0.91 (0.51), residues: 113 loop : -1.89 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 285 HIS 0.006 0.001 HIS A 268 PHE 0.012 0.001 PHE L 156 TYR 0.025 0.001 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 74 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.195 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 1.5964 time to fit residues: 113.1861 Evaluate side-chains 67 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.9578 time to fit residues: 4.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8135 moved from start: 0.1764 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= 0.283 Angle : 0.685 13.739 11395 Z= 0.311 Chirality : 0.043 0.153 1251 Planarity : 0.005 0.041 1317 Dihedral : 16.121 171.888 1260 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.54 % Allowed : 12.94 % Favored : 84.52 % 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: 576 sheet: 0.52 (0.50), residues: 119 loop : -1.91 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 285 HIS 0.008 0.002 HIS C 268 PHE 0.015 0.002 PHE H 108 TYR 0.028 0.002 TYR A 219 ARG 0.003 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 83 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.944 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 75 average time/residue: 1.4249 time to fit residues: 113.5194 Evaluate side-chains 68 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1078 time to fit residues: 1.3328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8130 moved from start: 0.1849 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= 0.271 Angle : 0.677 13.284 11395 Z= 0.306 Chirality : 0.042 0.149 1251 Planarity : 0.005 0.053 1317 Dihedral : 15.841 167.728 1260 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.54 % Allowed : 14.15 % Favored : 83.31 % 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: 0.46 (0.29), residues: 923 helix: 1.14 (0.23), residues: 576 sheet: 0.60 (0.50), residues: 117 loop : -1.97 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.009 0.002 HIS A 268 PHE 0.013 0.001 PHE B 170 TYR 0.027 0.002 TYR A 219 ARG 0.004 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 82 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.925 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 74 average time/residue: 1.2314 time to fit residues: 97.2819 Evaluate side-chains 71 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.3734 time to fit residues: 2.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.1913 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= 0.260 Angle : 0.668 13.173 11395 Z= 0.302 Chirality : 0.042 0.155 1251 Planarity : 0.005 0.048 1317 Dihedral : 15.548 167.803 1260 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: 0.53 (0.29), residues: 923 helix: 1.19 (0.23), residues: 570 sheet: 0.58 (0.50), residues: 118 loop : -1.80 (0.37), residues: 235 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 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 : 0.893 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 73 average time/residue: 1.1963 time to fit residues: 93.2272 Evaluate side-chains 69 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1162 time to fit residues: 1.6319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.1980 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= 0.255 Angle : 0.664 13.117 11395 Z= 0.300 Chirality : 0.042 0.154 1251 Planarity : 0.005 0.042 1317 Dihedral : 15.411 173.163 1260 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.42 % Allowed : 16.08 % 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: 0.53 (0.29), residues: 923 helix: 1.19 (0.23), residues: 570 sheet: 0.58 (0.50), residues: 118 loop : -1.82 (0.36), residues: 235 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 0.027 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: 20 poor density : 62 time to evaluate : 0.867 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 74 average time/residue: 1.1896 time to fit residues: 94.3053 Evaluate side-chains 69 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.2572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 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: 0.8099 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8324 Z= 0.215 Angle : 0.631 12.247 11395 Z= 0.285 Chirality : 0.041 0.148 1251 Planarity : 0.005 0.045 1317 Dihedral : 15.212 178.808 1260 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.81 % Allowed : 17.05 % Favored : 81.14 % 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: 0.70 (0.29), residues: 923 helix: 1.33 (0.24), residues: 570 sheet: 0.65 (0.50), residues: 118 loop : -1.79 (0.37), residues: 235 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 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 76 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.901 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 1.2383 time to fit residues: 93.7708 Evaluate side-chains 71 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.0807 time to fit residues: 3.4574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.2041 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= 0.256 Angle : 0.666 13.161 11395 Z= 0.301 Chirality : 0.042 0.152 1251 Planarity : 0.005 0.040 1317 Dihedral : 15.242 177.350 1260 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.81 % Allowed : 17.17 % Favored : 81.02 % 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: 0.57 (0.29), residues: 923 helix: 1.22 (0.23), residues: 570 sheet: 0.60 (0.50), residues: 118 loop : -1.81 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 247 HIS 0.008 0.002 HIS A 268 PHE 0.013 0.001 PHE B 170 TYR 0.027 0.002 TYR A 219 ARG 0.002 0.000 ARG A 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 77 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.964 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 1.2497 time to fit residues: 96.3135 Evaluate side-chains 73 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.4354 time to fit residues: 2.6857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 75 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105686 restraints weight = 9898.950| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.45 r_work: 0.3038 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8324 Z= 0.189 Angle : 0.609 11.641 11395 Z= 0.275 Chirality : 0.040 0.147 1251 Planarity : 0.005 0.043 1317 Dihedral : 14.923 169.968 1260 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.69 % Allowed : 17.17 % Favored : 81.14 % 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: 0.82 (0.29), residues: 923 helix: 1.44 (0.24), residues: 569 sheet: 0.72 (0.50), residues: 118 loop : -1.79 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP C 247 HIS 0.007 0.001 HIS A 268 PHE 0.011 0.001 PHE B 170 TYR 0.024 0.001 TYR B 219 ARG 0.002 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.92 seconds wall clock time: 52 minutes 17.53 seconds (3137.53 seconds total)