Starting phenix.real_space_refine on Thu Jun 12 00:57:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzj_41760/06_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_41760/06_2025/8tzj_41760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.cif" } resolution = 3.51 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 2, 'ASP:plan': 1} 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, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP: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, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP: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: 6.76, per 1000 atoms: 0.51 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: 3.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 4.79 Time building geometry restraints manager: 4.40 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 228 or resid 301 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: 0.730 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: 0.220 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.480 Find NCS groups from input model: 0.360 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.006 0.001 TRP C 48 HIS 0.002 0.001 HIS C 36 PHE 0.010 0.001 PHE C 32 TYR 0.008 0.001 TYR C 250 ARG 0.005 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.17082 ( 410) hydrogen bonds : angle 4.74411 ( 1206) covalent geometry : bond 0.00435 ( 6684) covalent geometry : angle 0.66960 ( 9050) *********************** 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 : 1.082 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: 0.6976 time to fit residues: 136.3330 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 : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.0010 chunk 76 optimal weight: 0.8980 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 193 ASN B 221 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111958 restraints weight = 27631.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116512 restraints weight = 13807.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119419 restraints weight = 8491.878| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6684 Z= 0.154 Angle : 0.608 6.588 9050 Z= 0.304 Chirality : 0.037 0.150 1074 Planarity : 0.004 0.037 1130 Dihedral : 8.576 114.794 940 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 7.94 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.29), residues: 834 helix: 2.49 (0.22), residues: 526 sheet: -0.67 (0.76), residues: 56 loop : -0.73 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 298 HIS 0.017 0.001 HIS A 97 PHE 0.015 0.001 PHE A 192 TYR 0.011 0.002 TYR C 250 ARG 0.005 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.06029 ( 410) hydrogen bonds : angle 4.32570 ( 1206) covalent geometry : bond 0.00346 ( 6684) covalent geometry : angle 0.60838 ( 9050) *********************** 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: 6 poor density : 91 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 LEU cc_start: 0.8304 (mt) cc_final: 0.8100 (tt) REVERT: D 300 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7217 (mt-10) outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.5289 time to fit residues: 63.8789 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 : 1.051 ------------------------------------------------------------------------------- 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 70 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 80 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 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 = 0.3640 r_free = 0.3640 target = 0.130357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112240 restraints weight = 27727.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116832 restraints weight = 13657.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119804 restraints weight = 8331.686| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6684 Z= 0.130 Angle : 0.529 6.494 9050 Z= 0.261 Chirality : 0.036 0.146 1074 Planarity : 0.003 0.031 1130 Dihedral : 8.058 118.170 940 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.32 % Allowed : 8.38 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.29), residues: 834 helix: 2.65 (0.22), residues: 526 sheet: -0.72 (0.74), residues: 56 loop : -0.65 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.012 0.001 HIS A 97 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR C 250 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 410) hydrogen bonds : angle 4.01606 ( 1206) covalent geometry : bond 0.00266 ( 6684) covalent geometry : angle 0.52881 ( 9050) *********************** 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 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 300 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7190 (mt-10) outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.5316 time to fit residues: 63.4671 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 : 0.926 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.127859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109776 restraints weight = 28004.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114262 restraints weight = 14056.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117145 restraints weight = 8618.595| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3428 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 : 0.535 6.041 9050 Z= 0.264 Chirality : 0.036 0.148 1074 Planarity : 0.004 0.062 1130 Dihedral : 8.019 120.816 940 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.92 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 (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: 2.28 (0.30), residues: 834 helix: 2.73 (0.22), residues: 526 sheet: -0.95 (0.71), residues: 56 loop : -0.60 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.010 0.001 HIS A 97 PHE 0.013 0.001 PHE D 189 TYR 0.011 0.002 TYR C 250 ARG 0.004 0.000 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 410) hydrogen bonds : angle 3.92368 ( 1206) covalent geometry : bond 0.00302 ( 6684) covalent geometry : angle 0.53488 ( 9050) *********************** 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 101 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.5346 time to fit residues: 68.5774 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 D residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.0000 chunk 80 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110432 restraints weight = 27858.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114894 restraints weight = 13818.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117811 restraints weight = 8349.550| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6684 Z= 0.114 Angle : 0.520 6.255 9050 Z= 0.254 Chirality : 0.036 0.145 1074 Planarity : 0.003 0.028 1130 Dihedral : 7.888 122.697 940 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.74 % Allowed : 10.59 % 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 (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: 2.41 (0.30), residues: 834 helix: 2.84 (0.22), residues: 526 sheet: -0.97 (0.71), residues: 56 loop : -0.53 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.008 0.001 HIS A 97 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR C 250 ARG 0.003 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 410) hydrogen bonds : angle 3.80202 ( 1206) covalent geometry : bond 0.00250 ( 6684) covalent geometry : angle 0.51981 ( 9050) *********************** 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 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.4814 time to fit residues: 57.6154 Evaluate side-chains 83 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 77 ASN 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 75 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** D 227 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 = 0.3561 r_free = 0.3561 target = 0.124516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105629 restraints weight = 28499.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110229 restraints weight = 14262.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113250 restraints weight = 8805.972| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6684 Z= 0.146 Angle : 0.538 6.013 9050 Z= 0.265 Chirality : 0.036 0.146 1074 Planarity : 0.003 0.027 1130 Dihedral : 7.985 126.425 940 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 (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: 2.36 (0.30), residues: 834 helix: 2.80 (0.22), residues: 526 sheet: -1.01 (0.70), residues: 56 loop : -0.54 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.007 0.001 HIS A 97 PHE 0.012 0.001 PHE D 189 TYR 0.011 0.001 TYR C 250 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 410) hydrogen bonds : angle 3.86819 ( 1206) covalent geometry : bond 0.00337 ( 6684) covalent geometry : angle 0.53810 ( 9050) *********************** 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 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.6399 time to fit residues: 76.2316 Evaluate side-chains 84 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 D residue 291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN ** D 227 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 = 0.3561 r_free = 0.3561 target = 0.124669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106177 restraints weight = 28133.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110682 restraints weight = 14300.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113620 restraints weight = 8843.942| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4003 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= 0.130 Angle : 0.535 6.013 9050 Z= 0.262 Chirality : 0.035 0.147 1074 Planarity : 0.003 0.025 1130 Dihedral : 7.953 127.734 940 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.88 % Allowed : 11.32 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.30), residues: 834 helix: 2.84 (0.22), residues: 526 sheet: -0.99 (0.71), residues: 56 loop : -0.55 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.006 0.001 HIS A 97 PHE 0.009 0.001 PHE D 32 TYR 0.011 0.001 TYR C 250 ARG 0.006 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 410) hydrogen bonds : angle 3.80505 ( 1206) covalent geometry : bond 0.00297 ( 6684) covalent geometry : angle 0.53489 ( 9050) *********************** 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 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 89 average time/residue: 0.7293 time to fit residues: 86.3565 Evaluate side-chains 87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 D residue 267 LEU 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 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105911 restraints weight = 28220.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110424 restraints weight = 14207.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113414 restraints weight = 8744.166| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4183 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 : 0.534 6.655 9050 Z= 0.260 Chirality : 0.036 0.147 1074 Planarity : 0.004 0.073 1130 Dihedral : 7.968 131.984 940 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.74 % Allowed : 11.47 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.30), residues: 834 helix: 2.88 (0.22), residues: 526 sheet: -0.96 (0.71), residues: 56 loop : -0.53 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 PHE 0.011 0.001 PHE B 13 TYR 0.011 0.001 TYR D 250 ARG 0.013 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 410) hydrogen bonds : angle 3.76074 ( 1206) covalent geometry : bond 0.00299 ( 6684) covalent geometry : angle 0.53392 ( 9050) *********************** 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 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.6220 time to fit residues: 75.2493 Evaluate side-chains 87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 D residue 267 LEU 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 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN ** D 285 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 = 0.3546 r_free = 0.3546 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104821 restraints weight = 28264.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109418 restraints weight = 14164.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112471 restraints weight = 8724.734| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4285 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= 0.135 Angle : 0.540 6.050 9050 Z= 0.266 Chirality : 0.036 0.146 1074 Planarity : 0.004 0.054 1130 Dihedral : 7.983 134.093 940 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.88 % Allowed : 11.91 % 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 (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: 2.49 (0.30), residues: 834 helix: 2.91 (0.22), residues: 526 sheet: -0.99 (0.71), residues: 56 loop : -0.52 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 298 HIS 0.005 0.001 HIS A 97 PHE 0.010 0.001 PHE B 13 TYR 0.011 0.001 TYR C 250 ARG 0.009 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 410) hydrogen bonds : angle 3.76819 ( 1206) covalent geometry : bond 0.00312 ( 6684) covalent geometry : angle 0.53974 ( 9050) *********************** 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 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 0.4925 time to fit residues: 56.9520 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 : 1.087 ------------------------------------------------------------------------------- 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 D residue 65 LEU Chi-restraints excluded: chain D residue 267 LEU 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 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN C 285 GLN D 225 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102960 restraints weight = 28438.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107353 restraints weight = 14533.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110257 restraints weight = 9077.834| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6684 Z= 0.188 Angle : 0.582 5.839 9050 Z= 0.291 Chirality : 0.037 0.148 1074 Planarity : 0.004 0.062 1130 Dihedral : 8.171 138.962 940 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.03 % Allowed : 12.06 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.30), residues: 834 helix: 2.75 (0.22), residues: 526 sheet: -1.26 (0.68), residues: 66 loop : -0.44 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 298 HIS 0.005 0.001 HIS A 97 PHE 0.014 0.001 PHE B 13 TYR 0.013 0.002 TYR D 250 ARG 0.010 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 410) hydrogen bonds : angle 3.93760 ( 1206) covalent geometry : bond 0.00448 ( 6684) covalent geometry : angle 0.58165 ( 9050) ********************** 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 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.5268 time to fit residues: 65.1843 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 D residue 65 LEU Chi-restraints excluded: chain D residue 267 LEU 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 55 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 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 ** D 285 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 = 0.3539 r_free = 0.3539 target = 0.123313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104834 restraints weight = 27911.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109247 restraints weight = 14043.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112254 restraints weight = 8727.439| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4557 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= 0.122 Angle : 0.541 6.229 9050 Z= 0.265 Chirality : 0.036 0.146 1074 Planarity : 0.004 0.056 1130 Dihedral : 7.997 137.618 940 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 (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: 2.47 (0.30), residues: 834 helix: 2.91 (0.22), residues: 526 sheet: -1.06 (0.70), residues: 56 loop : -0.55 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.006 0.001 HIS A 97 PHE 0.010 0.001 PHE C 32 TYR 0.010 0.001 TYR C 250 ARG 0.008 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 410) hydrogen bonds : angle 3.76075 ( 1206) covalent geometry : bond 0.00275 ( 6684) covalent geometry : angle 0.54084 ( 9050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4831.78 seconds wall clock time: 87 minutes 19.26 seconds (5239.26 seconds total)