Starting phenix.real_space_refine on Sat Aug 23 16:42:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzj_41760/08_2025/8tzj_41760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzj_41760/08_2025/8tzj_41760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzj_41760/08_2025/8tzj_41760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzj_41760/08_2025/8tzj_41760.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzj_41760/08_2025/8tzj_41760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzj_41760/08_2025/8tzj_41760.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4210 2.51 5 N 1184 2.21 5 O 1148 1.98 5 H 6772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13346 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3495 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3151 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3150 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.71, per 1000 atoms: 0.20 Number of scatterers: 13346 At special positions: 0 Unit cell: (70.2, 83.16, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 26 16.00 P 4 15.00 Mg 2 11.99 O 1148 8.00 N 1184 7.00 C 4210 6.00 H 6772 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 434.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 65.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.504A pdb=" N CYS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.851A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.980A pdb=" N GLU A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 178 through 196 removed outlier: 4.041A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.541A pdb=" N VAL A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.504A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.851A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.980A pdb=" N GLU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 178 through 196 removed outlier: 4.041A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.542A pdb=" N VAL B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 50 through 85 removed outlier: 3.739A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Proline residue: C 68 - end of helix Processing helix chain 'C' and resid 188 through 229 removed outlier: 3.836A pdb=" N ALA C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 240 removed outlier: 3.507A pdb=" N GLY C 240 " --> pdb=" O MET C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 287 Proline residue: C 249 - end of helix removed outlier: 4.135A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.676A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 48 removed outlier: 4.254A pdb=" N TRP D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 85 removed outlier: 3.870A pdb=" N LEU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 188 through 229 removed outlier: 3.509A pdb=" N ASP D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 242 through 288 Proline residue: D 249 - end of helix removed outlier: 4.049A pdb=" N GLY D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.697A pdb=" N ALA D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.900A pdb=" N ILE A 11 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 6.351A pdb=" N VAL A 16 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 29 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 27 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.045A pdb=" N ALA A 40 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 170 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY A 91 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 171 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 93 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.739A pdb=" N GLY A 43 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.901A pdb=" N ILE B 11 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.351A pdb=" N VAL B 16 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 29 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 27 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.045A pdb=" N ALA B 40 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 170 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY B 91 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.738A pdb=" N GLY B 43 " --> pdb=" O LEU B 220 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1206 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: 2.58 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6766 1.03 - 1.23: 28 1.23 - 1.42: 2664 1.42 - 1.61: 3946 1.61 - 1.81: 52 Bond restraints: 13456 Sorted by residual: bond pdb=" C4 ADP B 302 " pdb=" C5 ADP B 302 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 ADP A 302 " pdb=" C5 ADP A 302 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C6 ADP B 302 " pdb=" N6 ADP B 302 " ideal model delta sigma weight residual 1.355 1.447 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C6 ADP A 302 " pdb=" N6 ADP A 302 " ideal model delta sigma weight residual 1.355 1.447 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C5 ADP B 302 " pdb=" C6 ADP B 302 " ideal model delta sigma weight residual 1.490 1.415 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 13451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 22783 2.06 - 4.12: 1498 4.12 - 6.17: 78 6.17 - 8.23: 6 8.23 - 10.29: 12 Bond angle restraints: 24377 Sorted by residual: angle pdb=" N LYS B 50 " pdb=" CA LYS B 50 " pdb=" C LYS B 50 " ideal model delta sigma weight residual 111.07 115.88 -4.81 1.07e+00 8.73e-01 2.02e+01 angle pdb=" N LYS A 50 " pdb=" CA LYS A 50 " pdb=" C LYS A 50 " ideal model delta sigma weight residual 111.07 115.85 -4.78 1.07e+00 8.73e-01 2.00e+01 angle pdb=" N GLN B 25 " pdb=" CA GLN B 25 " pdb=" C GLN B 25 " ideal model delta sigma weight residual 108.52 115.37 -6.85 1.63e+00 3.76e-01 1.76e+01 angle pdb=" N GLN A 25 " pdb=" CA GLN A 25 " pdb=" C GLN A 25 " ideal model delta sigma weight residual 108.52 115.34 -6.82 1.63e+00 3.76e-01 1.75e+01 angle pdb=" CA ALA A 48 " pdb=" C ALA A 48 " pdb=" N GLY A 49 " ideal model delta sigma weight residual 117.19 122.78 -5.59 1.50e+00 4.44e-01 1.39e+01 ... (remaining 24372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.57: 5969 26.57 - 53.14: 206 53.14 - 79.71: 35 79.71 - 106.28: 4 106.28 - 132.85: 2 Dihedral angle restraints: 6216 sinusoidal: 3431 harmonic: 2785 Sorted by residual: dihedral pdb=" O2A ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PA ADP A 302 " pdb=" PB ADP A 302 " ideal model delta sinusoidal sigma weight residual -60.00 72.85 -132.85 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PA ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 72.82 -132.82 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O1B ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " pdb=" PA ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 45.65 -105.66 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 6213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 920 0.051 - 0.103: 122 0.103 - 0.154: 26 0.154 - 0.206: 2 0.206 - 0.257: 4 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C3' ADP A 302 " pdb=" C2' ADP A 302 " pdb=" C4' ADP A 302 " pdb=" O3' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' ADP B 302 " pdb=" C2' ADP B 302 " pdb=" C4' ADP B 302 " pdb=" O3' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2' ADP B 302 " pdb=" C1' ADP B 302 " pdb=" C3' ADP B 302 " pdb=" O2' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1071 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 18 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C LYS A 18 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 18 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 19 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 18 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C LYS B 18 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 18 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 44 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS A 45 " -0.010 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 230 2.11 - 2.73: 24131 2.73 - 3.36: 36922 3.36 - 3.98: 44593 3.98 - 4.60: 72553 Nonbonded interactions: 178429 Sorted by model distance: nonbonded pdb=" HD1 HIS D 36 " pdb=" OH TYR D 252 " model vdw 1.490 2.450 nonbonded pdb=" HD1 HIS C 36 " pdb=" OH TYR C 252 " model vdw 1.537 2.450 nonbonded pdb=" HE2 PHE B 13 " pdb="HD11 LEU B 53 " model vdw 1.550 2.270 nonbonded pdb=" HE2 PHE A 13 " pdb="HD11 LEU A 53 " model vdw 1.551 2.270 nonbonded pdb=" O ALA D 59 " pdb=" HG SER D 62 " model vdw 1.645 2.450 ... (remaining 178424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 9 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 52 through 302)) } ncs_group { reference = (chain 'C' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 37 through 330)) selection = chain 'D' } 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: 1.510 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.004 0.097 6684 Z= 0.232 Angle : 0.670 10.288 9050 Z= 0.341 Chirality : 0.040 0.257 1074 Planarity : 0.003 0.026 1130 Dihedral : 12.126 132.849 2450 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.30), residues: 834 helix: 2.73 (0.23), residues: 508 sheet: -0.71 (0.77), residues: 56 loop : -0.67 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 126 TYR 0.008 0.001 TYR C 250 PHE 0.010 0.001 PHE C 32 TRP 0.006 0.001 TRP C 48 HIS 0.002 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6684) covalent geometry : angle 0.66960 ( 9050) hydrogen bonds : bond 0.17082 ( 410) hydrogen bonds : angle 4.74411 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8343 (mttt) cc_final: 0.8130 (mttm) REVERT: C 212 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpt) REVERT: C 302 LEU cc_start: 0.8034 (mt) cc_final: 0.7659 (tt) REVERT: D 76 LYS cc_start: 0.8437 (tttt) cc_final: 0.8229 (tptt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2827 time to fit residues: 54.7967 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.0010 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN B 80 ASN B 193 ASN B 210 ASN B 221 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111826 restraints weight = 27599.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116398 restraints weight = 13793.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119395 restraints weight = 8485.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121403 restraints weight = 5865.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122621 restraints weight = 4393.607| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6684 Z= 0.158 Angle : 0.604 6.762 9050 Z= 0.303 Chirality : 0.037 0.151 1074 Planarity : 0.004 0.037 1130 Dihedral : 8.563 115.222 940 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.03 % Allowed : 8.09 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.29), residues: 834 helix: 2.49 (0.22), residues: 526 sheet: -0.66 (0.76), residues: 56 loop : -0.73 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 21 TYR 0.011 0.002 TYR C 250 PHE 0.015 0.001 PHE D 37 TRP 0.004 0.001 TRP C 298 HIS 0.020 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6684) covalent geometry : angle 0.60423 ( 9050) hydrogen bonds : bond 0.05913 ( 410) hydrogen bonds : angle 4.31887 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 LEU cc_start: 0.8278 (mt) cc_final: 0.8076 (tt) REVERT: D 300 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7150 (mt-10) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.2065 time to fit residues: 24.4992 Evaluate side-chains 83 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112239 restraints weight = 27804.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116695 restraints weight = 13980.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119579 restraints weight = 8572.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121443 restraints weight = 5943.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122790 restraints weight = 4481.055| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6684 Z= 0.129 Angle : 0.532 6.538 9050 Z= 0.262 Chirality : 0.036 0.146 1074 Planarity : 0.003 0.030 1130 Dihedral : 8.079 118.434 940 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 8.38 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.29), residues: 834 helix: 2.64 (0.22), residues: 526 sheet: -0.73 (0.74), residues: 56 loop : -0.64 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.010 0.001 TYR C 250 PHE 0.009 0.001 PHE D 32 TRP 0.004 0.001 TRP C 298 HIS 0.012 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6684) covalent geometry : angle 0.53205 ( 9050) hydrogen bonds : bond 0.05195 ( 410) hydrogen bonds : angle 4.01903 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 300 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7046 (mt-10) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.2074 time to fit residues: 24.4100 Evaluate side-chains 85 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110593 restraints weight = 27717.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114972 restraints weight = 13785.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117783 restraints weight = 8464.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119709 restraints weight = 5855.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121033 restraints weight = 4384.861| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6684 Z= 0.131 Angle : 0.529 6.084 9050 Z= 0.261 Chirality : 0.036 0.148 1074 Planarity : 0.003 0.040 1130 Dihedral : 8.030 119.352 940 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.18 % Allowed : 9.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.30), residues: 834 helix: 2.72 (0.22), residues: 526 sheet: -0.84 (0.72), residues: 56 loop : -0.62 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 223 TYR 0.010 0.001 TYR C 250 PHE 0.016 0.001 PHE D 37 TRP 0.005 0.001 TRP C 298 HIS 0.009 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6684) covalent geometry : angle 0.52916 ( 9050) hydrogen bonds : bond 0.04801 ( 410) hydrogen bonds : angle 3.94857 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.1981 time to fit residues: 22.9834 Evaluate side-chains 86 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108643 restraints weight = 27926.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113250 restraints weight = 13977.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116264 restraints weight = 8554.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118218 restraints weight = 5914.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119628 restraints weight = 4482.123| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6684 Z= 0.145 Angle : 0.540 6.107 9050 Z= 0.266 Chirality : 0.036 0.150 1074 Planarity : 0.003 0.030 1130 Dihedral : 8.003 123.837 940 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.03 % Allowed : 10.29 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.30), residues: 834 helix: 2.78 (0.22), residues: 526 sheet: -1.23 (0.68), residues: 66 loop : -0.33 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.012 0.002 TYR C 250 PHE 0.021 0.001 PHE D 37 TRP 0.006 0.001 TRP C 298 HIS 0.008 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6684) covalent geometry : angle 0.53988 ( 9050) hydrogen bonds : bond 0.04671 ( 410) hydrogen bonds : angle 3.92259 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: D 300 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7163 (mt-10) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.2084 time to fit residues: 26.0331 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106820 restraints weight = 27903.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111239 restraints weight = 13986.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114136 restraints weight = 8616.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115884 restraints weight = 6001.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117314 restraints weight = 4643.657| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6684 Z= 0.136 Angle : 0.532 6.119 9050 Z= 0.261 Chirality : 0.036 0.145 1074 Planarity : 0.004 0.051 1130 Dihedral : 8.007 126.756 940 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.18 % Allowed : 11.18 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.30), residues: 834 helix: 2.80 (0.22), residues: 526 sheet: -1.14 (0.70), residues: 56 loop : -0.56 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.011 0.001 TYR C 250 PHE 0.010 0.001 PHE C 215 TRP 0.005 0.001 TRP C 298 HIS 0.007 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6684) covalent geometry : angle 0.53244 ( 9050) hydrogen bonds : bond 0.04556 ( 410) hydrogen bonds : angle 3.86581 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.233 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1888 time to fit residues: 22.0882 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN D 225 ASN D 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107315 restraints weight = 27770.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111745 restraints weight = 13909.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114651 restraints weight = 8520.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116349 restraints weight = 5926.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117797 restraints weight = 4595.799| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6684 Z= 0.122 Angle : 0.530 6.162 9050 Z= 0.260 Chirality : 0.036 0.145 1074 Planarity : 0.003 0.045 1130 Dihedral : 7.973 128.008 940 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.18 % Allowed : 11.62 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.30), residues: 834 helix: 2.82 (0.22), residues: 526 sheet: -1.10 (0.70), residues: 56 loop : -0.55 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.010 0.001 TYR C 250 PHE 0.010 0.001 PHE B 13 TRP 0.006 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6684) covalent geometry : angle 0.53005 ( 9050) hydrogen bonds : bond 0.04478 ( 410) hydrogen bonds : angle 3.82181 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: D 325 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8322 (mtmm) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.1792 time to fit residues: 22.4456 Evaluate side-chains 86 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 63 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110180 restraints weight = 27458.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114749 restraints weight = 13665.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117827 restraints weight = 8356.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119610 restraints weight = 5740.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121150 restraints weight = 4423.363| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6684 Z= 0.104 Angle : 0.518 6.237 9050 Z= 0.252 Chirality : 0.035 0.144 1074 Planarity : 0.003 0.038 1130 Dihedral : 7.830 129.272 940 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.59 % Allowed : 12.06 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.30), residues: 834 helix: 2.95 (0.22), residues: 526 sheet: -1.02 (0.71), residues: 56 loop : -0.52 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.009 0.001 TYR C 250 PHE 0.010 0.001 PHE C 32 TRP 0.006 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6684) covalent geometry : angle 0.51763 ( 9050) hydrogen bonds : bond 0.04193 ( 410) hydrogen bonds : angle 3.66837 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.346 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 90 average time/residue: 0.1972 time to fit residues: 22.6460 Evaluate side-chains 88 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN D 225 ASN D 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104619 restraints weight = 28429.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109244 restraints weight = 14291.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112189 restraints weight = 8830.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114262 restraints weight = 6175.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115540 restraints weight = 4672.822| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6684 Z= 0.138 Angle : 0.545 6.333 9050 Z= 0.266 Chirality : 0.036 0.145 1074 Planarity : 0.004 0.058 1130 Dihedral : 7.978 135.605 940 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.88 % Allowed : 12.35 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.30), residues: 834 helix: 2.91 (0.22), residues: 526 sheet: -1.04 (0.71), residues: 56 loop : -0.58 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 292 TYR 0.014 0.001 TYR D 250 PHE 0.011 0.001 PHE B 13 TRP 0.007 0.001 TRP C 298 HIS 0.006 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6684) covalent geometry : angle 0.54540 ( 9050) hydrogen bonds : bond 0.04287 ( 410) hydrogen bonds : angle 3.76425 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: D 324 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8167 (mp) outliers start: 6 outliers final: 5 residues processed: 94 average time/residue: 0.1877 time to fit residues: 22.6460 Evaluate side-chains 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104712 restraints weight = 28132.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109191 restraints weight = 14332.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112166 restraints weight = 8879.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113986 restraints weight = 6230.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.115454 restraints weight = 4812.020| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6684 Z= 0.131 Angle : 0.538 6.108 9050 Z= 0.264 Chirality : 0.036 0.147 1074 Planarity : 0.003 0.041 1130 Dihedral : 7.983 139.575 940 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.59 % Allowed : 12.65 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.30), residues: 834 helix: 2.94 (0.22), residues: 526 sheet: -1.04 (0.71), residues: 56 loop : -0.56 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 292 TYR 0.010 0.001 TYR C 250 PHE 0.011 0.001 PHE B 13 TRP 0.008 0.001 TRP C 298 HIS 0.006 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6684) covalent geometry : angle 0.53817 ( 9050) hydrogen bonds : bond 0.04290 ( 410) hydrogen bonds : angle 3.73473 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: C 232 GLU cc_start: 0.7048 (tt0) cc_final: 0.6688 (tt0) outliers start: 4 outliers final: 4 residues processed: 94 average time/residue: 0.2078 time to fit residues: 24.2734 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105084 restraints weight = 28019.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109634 restraints weight = 14003.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112706 restraints weight = 8658.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114569 restraints weight = 6014.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116060 restraints weight = 4629.947| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6684 Z= 0.117 Angle : 0.538 6.212 9050 Z= 0.264 Chirality : 0.035 0.145 1074 Planarity : 0.005 0.099 1130 Dihedral : 7.955 140.562 940 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.74 % Allowed : 12.50 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.30), residues: 834 helix: 2.97 (0.22), residues: 526 sheet: -1.16 (0.69), residues: 56 loop : -0.48 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 21 TYR 0.010 0.001 TYR D 250 PHE 0.013 0.001 PHE D 37 TRP 0.007 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6684) covalent geometry : angle 0.53767 ( 9050) hydrogen bonds : bond 0.04197 ( 410) hydrogen bonds : angle 3.68678 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1829.19 seconds wall clock time: 31 minutes 46.96 seconds (1906.96 seconds total)