Starting phenix.real_space_refine on Mon Mar 11 06:28:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/03_2024/5h1b_9566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/03_2024/5h1b_9566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/03_2024/5h1b_9566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/03_2024/5h1b_9566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/03_2024/5h1b_9566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/03_2024/5h1b_9566_updated.pdb" } resolution = 4.4 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= 0.002 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 P 18 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4557 2.51 5 N 1287 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 170": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" 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: 7359 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2361 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.42, per 1000 atoms: 0.60 Number of scatterers: 7359 At special positions: 0 Unit cell: (107.092, 69.218, 116.234, 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) S 39 16.00 P 18 15.00 Mg 3 11.99 O 1455 8.00 N 1287 7.00 C 4557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.26 Conformation dependent library (CDL) restraints added in 1.2 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 6 sheets defined 44.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.606A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.713A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.768A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.100A pdb=" N ASP A 231 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.602A pdb=" N ARG A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.698A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.606A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 81 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.713A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 197 through 213 removed outlier: 3.768A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.101A pdb=" N ASP B 231 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.602A pdb=" N ARG B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.698A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.606A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 68 through 81 Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 133 through 145 removed outlier: 4.712A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.768A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.100A pdb=" N ASP C 231 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.602A pdb=" N ARG C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 251 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.698A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 122 through 127 removed outlier: 7.224A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY A 127 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 267 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA A 190 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP A 161 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A 192 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 299 through 304 Processing sheet with id= C, first strand: chain 'B' and resid 122 through 127 removed outlier: 7.224A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY B 127 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN B 267 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA B 190 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP B 161 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 192 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 299 through 304 Processing sheet with id= E, first strand: chain 'C' and resid 122 through 127 removed outlier: 7.225A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLY C 127 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 267 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA C 190 " --> pdb=" O TYR C 159 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP C 161 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA C 192 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 299 through 304 258 hydrogen bonds defined for protein. 729 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: 1.96 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2372 1.33 - 1.45: 1159 1.45 - 1.57: 3854 1.57 - 1.69: 33 1.69 - 1.81: 63 Bond restraints: 7481 Sorted by residual: bond pdb=" O3A ANP A 600 " pdb=" PB ANP A 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3A ANP B 600 " pdb=" PB ANP B 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" O3A ANP C 600 " pdb=" PB ANP C 600 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N3B ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N3B ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 7476 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.27: 173 105.27 - 112.04: 3660 112.04 - 118.81: 2356 118.81 - 125.58: 3893 125.58 - 132.35: 63 Bond angle restraints: 10145 Sorted by residual: angle pdb=" PB ANP C 600 " pdb=" N3B ANP C 600 " pdb=" PG ANP C 600 " ideal model delta sigma weight residual 126.95 108.18 18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" PB ANP B 600 " pdb=" N3B ANP B 600 " pdb=" PG ANP B 600 " ideal model delta sigma weight residual 126.95 108.18 18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" PB ANP A 600 " pdb=" N3B ANP A 600 " pdb=" PG ANP A 600 " ideal model delta sigma weight residual 126.95 108.20 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 111.71 105.46 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" N THR B 197 " pdb=" CA THR B 197 " pdb=" C THR B 197 " ideal model delta sigma weight residual 111.71 105.47 6.24 1.15e+00 7.56e-01 2.94e+01 ... (remaining 10140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 4322 23.74 - 47.48: 162 47.48 - 71.22: 46 71.22 - 94.96: 27 94.96 - 118.70: 3 Dihedral angle restraints: 4560 sinusoidal: 1926 harmonic: 2634 Sorted by residual: dihedral pdb=" CA CYS C 319 " pdb=" C CYS C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA CYS B 319 " pdb=" C CYS B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA CYS A 319 " pdb=" C CYS A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta harmonic sigma weight residual 180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 4557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 888 0.064 - 0.129: 244 0.129 - 0.193: 23 0.193 - 0.257: 0 0.257 - 0.321: 3 Chirality restraints: 1158 Sorted by residual: chirality pdb=" C3' ANP C 600 " pdb=" C2' ANP C 600 " pdb=" C4' ANP C 600 " pdb=" O3' ANP C 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C3' ANP B 600 " pdb=" C2' ANP B 600 " pdb=" C4' ANP B 600 " pdb=" O3' ANP B 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C3' ANP A 600 " pdb=" C2' ANP A 600 " pdb=" C4' ANP A 600 " pdb=" O3' ANP A 600 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1155 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 246 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA A 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 247 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 246 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ALA B 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 247 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 246 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ALA C 246 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 246 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 247 " -0.013 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 46 2.18 - 2.86: 3060 2.86 - 3.54: 11410 3.54 - 4.22: 18728 4.22 - 4.90: 29915 Nonbonded interactions: 63159 Sorted by model distance: nonbonded pdb=" CB ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.503 3.460 nonbonded pdb=" CA ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.572 3.470 nonbonded pdb=" N ALA A 271 " pdb=" OP2 DT D 4 " model vdw 1.580 2.520 nonbonded pdb=" OH TYR B 159 " pdb=" OD2 ASP B 222 " model vdw 1.586 2.440 nonbonded pdb=" OH TYR A 159 " pdb=" OD2 ASP A 222 " model vdw 1.586 2.440 ... (remaining 63154 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' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 3.790 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.780 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 : 0.010 0.150 7481 Z= 0.660 Angle : 1.411 18.767 10145 Z= 0.917 Chirality : 0.056 0.321 1158 Planarity : 0.005 0.034 1272 Dihedral : 16.126 118.695 2874 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 54.25 Ramachandran Plot: Outliers : 2.63 % Allowed : 6.25 % Favored : 91.12 % Rotamer: Outliers : 5.67 % Allowed : 2.43 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -1.51 (0.27), residues: 912 helix: -2.43 (0.18), residues: 378 sheet: -0.80 (0.40), residues: 159 loop : 0.92 (0.36), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 138 PHE 0.018 0.003 PHE C 86 TYR 0.019 0.002 TYR A 315 ARG 0.010 0.002 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6302 (mp) REVERT: A 265 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8424 (mm) REVERT: B 62 ASN cc_start: 0.7700 (m-40) cc_final: 0.7444 (m110) REVERT: B 99 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6453 (mp) REVERT: B 170 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6648 (mpt180) REVERT: B 265 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8012 (mm) outliers start: 42 outliers final: 13 residues processed: 132 average time/residue: 0.2893 time to fit residues: 46.9606 Evaluate side-chains 72 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7481 Z= 0.297 Angle : 0.750 7.568 10145 Z= 0.401 Chirality : 0.043 0.167 1158 Planarity : 0.004 0.036 1272 Dihedral : 13.365 114.427 1191 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.82 % Favored : 93.86 % Rotamer: Outliers : 0.40 % Allowed : 0.67 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.42 (0.28), residues: 912 helix: -0.51 (0.24), residues: 411 sheet: -0.65 (0.40), residues: 162 loop : 0.61 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 294 PHE 0.020 0.002 PHE B 126 TYR 0.017 0.001 TYR B 315 ARG 0.008 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.6195 (mp) REVERT: B 62 ASN cc_start: 0.7520 (m-40) cc_final: 0.7269 (m110) REVERT: B 99 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6404 (mp) REVERT: B 225 THR cc_start: 0.8439 (p) cc_final: 0.7808 (p) REVERT: C 301 TYR cc_start: 0.7642 (t80) cc_final: 0.7411 (t80) outliers start: 3 outliers final: 0 residues processed: 68 average time/residue: 0.2410 time to fit residues: 21.9399 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7481 Z= 0.189 Angle : 0.624 7.432 10145 Z= 0.332 Chirality : 0.039 0.155 1158 Planarity : 0.003 0.027 1272 Dihedral : 11.939 105.974 1191 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 1.32 % Allowed : 4.61 % Favored : 94.08 % Rotamer: Outliers : 0.40 % Allowed : 1.75 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.26 (0.28), residues: 912 helix: 0.48 (0.24), residues: 414 sheet: -0.65 (0.39), residues: 165 loop : 0.55 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 294 PHE 0.017 0.002 PHE B 86 TYR 0.021 0.001 TYR C 315 ARG 0.004 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 99 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6435 (mp) REVERT: B 205 TYR cc_start: 0.7201 (m-80) cc_final: 0.6968 (m-10) REVERT: B 267 ASN cc_start: 0.7742 (p0) cc_final: 0.7532 (p0) REVERT: B 301 TYR cc_start: 0.6732 (t80) cc_final: 0.6455 (t80) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 0.1919 time to fit residues: 17.3919 Evaluate side-chains 38 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7481 Z= 0.325 Angle : 0.690 7.480 10145 Z= 0.366 Chirality : 0.040 0.179 1158 Planarity : 0.004 0.044 1272 Dihedral : 12.125 107.141 1191 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 1.32 % Allowed : 5.04 % Favored : 93.64 % Rotamer: Outliers : 0.13 % Allowed : 2.97 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.07 (0.27), residues: 912 helix: 0.73 (0.24), residues: 420 sheet: -0.57 (0.42), residues: 144 loop : -0.34 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 294 PHE 0.020 0.002 PHE C 195 TYR 0.018 0.002 TYR C 315 ARG 0.006 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 99 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6134 (mp) REVERT: B 267 ASN cc_start: 0.8055 (p0) cc_final: 0.7760 (p0) REVERT: C 251 MET cc_start: 0.7690 (tpt) cc_final: 0.7482 (tpt) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1748 time to fit residues: 11.6132 Evaluate side-chains 35 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7481 Z= 0.292 Angle : 0.650 7.777 10145 Z= 0.342 Chirality : 0.039 0.176 1158 Planarity : 0.004 0.040 1272 Dihedral : 12.128 109.009 1191 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.93 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.12 (0.27), residues: 912 helix: 0.95 (0.25), residues: 420 sheet: -0.72 (0.41), residues: 144 loop : -0.48 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 138 PHE 0.016 0.002 PHE B 126 TYR 0.012 0.001 TYR B 191 ARG 0.005 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.801 Fit side-chains REVERT: B 158 MET cc_start: 0.7030 (pmm) cc_final: 0.6704 (pmm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1707 time to fit residues: 12.0778 Evaluate side-chains 38 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7481 Z= 0.304 Angle : 0.665 8.567 10145 Z= 0.347 Chirality : 0.040 0.181 1158 Planarity : 0.004 0.056 1272 Dihedral : 12.217 110.409 1191 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 1.21 % Allowed : 5.15 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.02 (0.27), residues: 912 helix: 0.82 (0.24), residues: 423 sheet: -0.77 (0.40), residues: 144 loop : -0.57 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 294 PHE 0.017 0.002 PHE C 195 TYR 0.014 0.001 TYR B 191 ARG 0.005 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.896 Fit side-chains REVERT: B 205 TYR cc_start: 0.7279 (m-10) cc_final: 0.7037 (m-10) REVERT: B 219 LEU cc_start: 0.8479 (mm) cc_final: 0.8271 (mt) REVERT: B 267 ASN cc_start: 0.8088 (p0) cc_final: 0.7886 (p0) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1701 time to fit residues: 12.5669 Evaluate side-chains 36 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.0170 chunk 51 optimal weight: 9.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7481 Z= 0.186 Angle : 0.601 7.750 10145 Z= 0.311 Chirality : 0.039 0.170 1158 Planarity : 0.003 0.050 1272 Dihedral : 11.919 110.249 1191 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 1.21 % Allowed : 4.39 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.38 (0.28), residues: 912 helix: 1.17 (0.25), residues: 423 sheet: -0.53 (0.42), residues: 144 loop : -0.42 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 47 PHE 0.020 0.002 PHE B 259 TYR 0.012 0.001 TYR B 191 ARG 0.003 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: B 158 MET cc_start: 0.7320 (pmm) cc_final: 0.6878 (ptp) REVERT: B 205 TYR cc_start: 0.7358 (m-10) cc_final: 0.6971 (m-10) REVERT: B 219 LEU cc_start: 0.8212 (mm) cc_final: 0.7912 (mt) REVERT: B 267 ASN cc_start: 0.8052 (p0) cc_final: 0.7837 (p0) REVERT: C 58 LYS cc_start: 0.7958 (pttp) cc_final: 0.7704 (ptpt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1856 time to fit residues: 13.7105 Evaluate side-chains 41 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 0.0370 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7481 Z= 0.323 Angle : 0.697 8.383 10145 Z= 0.357 Chirality : 0.041 0.182 1158 Planarity : 0.005 0.069 1272 Dihedral : 12.181 110.853 1191 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.04 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.04 (0.27), residues: 912 helix: 0.84 (0.25), residues: 420 sheet: -0.58 (0.42), residues: 144 loop : -0.56 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 294 PHE 0.022 0.002 PHE B 86 TYR 0.016 0.002 TYR B 191 ARG 0.007 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: B 267 ASN cc_start: 0.7978 (p0) cc_final: 0.7694 (p0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1707 time to fit residues: 11.9429 Evaluate side-chains 36 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7481 Z= 0.246 Angle : 0.636 7.831 10145 Z= 0.328 Chirality : 0.039 0.178 1158 Planarity : 0.004 0.049 1272 Dihedral : 12.017 111.105 1191 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.71 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.16 (0.28), residues: 912 helix: 0.98 (0.25), residues: 423 sheet: -0.51 (0.42), residues: 144 loop : -0.61 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 138 PHE 0.019 0.002 PHE B 86 TYR 0.016 0.001 TYR B 191 ARG 0.007 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 158 MET cc_start: 0.7252 (pmm) cc_final: 0.6905 (ptp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1677 time to fit residues: 12.0135 Evaluate side-chains 38 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7481 Z= 0.200 Angle : 0.614 7.931 10145 Z= 0.315 Chirality : 0.039 0.173 1158 Planarity : 0.003 0.044 1272 Dihedral : 11.755 111.391 1191 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.71 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 0.40 (0.28), residues: 912 helix: 1.20 (0.25), residues: 423 sheet: -0.52 (0.42), residues: 147 loop : -0.42 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 294 PHE 0.020 0.002 PHE C 86 TYR 0.013 0.001 TYR B 191 ARG 0.006 0.000 ARG B 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 267 ASN cc_start: 0.7974 (p0) cc_final: 0.7722 (p0) REVERT: C 58 LYS cc_start: 0.7753 (pttp) cc_final: 0.7514 (ptpt) REVERT: C 158 MET cc_start: 0.7264 (pmm) cc_final: 0.6820 (ptp) REVERT: C 225 THR cc_start: 0.7845 (p) cc_final: 0.7101 (p) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1840 time to fit residues: 13.9190 Evaluate side-chains 42 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.033793 restraints weight = 53984.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.034855 restraints weight = 30248.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035610 restraints weight = 19260.141| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7481 Z= 0.208 Angle : 0.615 8.040 10145 Z= 0.315 Chirality : 0.039 0.173 1158 Planarity : 0.003 0.044 1272 Dihedral : 11.653 110.672 1191 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.71 % Favored : 94.41 % Rotamer: Outliers : 0.13 % Allowed : 0.00 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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 (0.28), residues: 912 helix: 1.31 (0.25), residues: 408 sheet: -0.46 (0.42), residues: 147 loop : -0.21 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 294 PHE 0.018 0.002 PHE C 86 TYR 0.014 0.001 TYR B 191 ARG 0.007 0.000 ARG B 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1362.96 seconds wall clock time: 26 minutes 10.27 seconds (1570.27 seconds total)