Starting phenix.real_space_refine on Sun Jul 21 05:15:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/07_2024/8tzj_41760_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/07_2024/8tzj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/07_2024/8tzj_41760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/07_2024/8tzj_41760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/07_2024/8tzj_41760_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/07_2024/8tzj_41760_neut.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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.72, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.64 Conformation dependent library (CDL) restraints added in 1.5 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: 1.02 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: 4.54 Time building geometry restraints manager: 11.25 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: 99.65 - 106.62: 269 106.62 - 113.59: 16057 113.59 - 120.56: 4824 120.56 - 127.53: 3165 127.53 - 134.50: 62 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 1.850 nonbonded pdb=" HD1 HIS C 36 " pdb=" OH TYR C 252 " model vdw 1.537 1.850 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 1.850 ... (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 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: 1.040 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: 0.190 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.370 Find NCS groups from input model: 0.460 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.590 ------------------------------------------------------------------------------- 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= 0.301 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.045 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: 0.6925 time to fit residues: 135.3197 Evaluate side-chains 90 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.0040 chunk 76 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6684 Z= 0.243 Angle : 0.595 6.242 9050 Z= 0.296 Chirality : 0.037 0.150 1074 Planarity : 0.004 0.029 1130 Dihedral : 8.509 123.222 940 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 2.03 (0.29), residues: 834 helix: 2.50 (0.22), residues: 526 sheet: -0.66 (0.76), residues: 56 loop : -0.72 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 298 HIS 0.020 0.002 HIS A 97 PHE 0.015 0.001 PHE D 37 TYR 0.011 0.002 TYR C 250 ARG 0.004 0.000 ARG B 21 *********************** 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 96 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8348 (mttt) cc_final: 0.8120 (mtmt) REVERT: B 39 MET cc_start: 0.8181 (ttt) cc_final: 0.7980 (ttp) REVERT: C 302 LEU cc_start: 0.8150 (mt) cc_final: 0.7926 (tt) REVERT: D 76 LYS cc_start: 0.8328 (tttt) cc_final: 0.8041 (tptt) REVERT: D 300 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7602 (mt-10) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.5300 time to fit residues: 63.3398 Evaluate side-chains 85 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 190 GLU Chi-restraints excluded: chain C residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2976 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= 0.228 Angle : 0.543 6.143 9050 Z= 0.269 Chirality : 0.036 0.147 1074 Planarity : 0.003 0.030 1130 Dihedral : 8.251 131.564 940 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.62 % Allowed : 9.12 % Favored : 89.26 % 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 (0.29), residues: 834 helix: 2.58 (0.22), residues: 526 sheet: -0.89 (0.71), residues: 66 loop : -0.48 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 298 HIS 0.012 0.001 HIS A 97 PHE 0.010 0.001 PHE C 215 TYR 0.011 0.001 TYR C 250 ARG 0.002 0.000 ARG C 223 *********************** 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 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8240 (mttt) cc_final: 0.8016 (mtmt) REVERT: B 39 MET cc_start: 0.8264 (ttt) cc_final: 0.8031 (ttp) REVERT: B 180 GLU cc_start: 0.7954 (tp30) cc_final: 0.7630 (tp30) REVERT: C 302 LEU cc_start: 0.8199 (mt) cc_final: 0.7927 (tt) REVERT: D 76 LYS cc_start: 0.8254 (tttt) cc_final: 0.8022 (tptt) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.5496 time to fit residues: 62.4078 Evaluate side-chains 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 208 SER Chi-restraints excluded: chain D residue 193 ASP 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 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6684 Z= 0.249 Angle : 0.550 6.030 9050 Z= 0.272 Chirality : 0.036 0.150 1074 Planarity : 0.004 0.072 1130 Dihedral : 8.287 145.350 940 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.47 % Allowed : 9.41 % Favored : 89.12 % 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: 2.12 (0.29), residues: 834 helix: 2.57 (0.22), residues: 526 sheet: -1.20 (0.69), residues: 66 loop : -0.47 (0.39), residues: 242 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 0.014 0.001 PHE D 189 TYR 0.012 0.001 TYR C 250 ARG 0.004 0.000 ARG D 223 *********************** 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 105 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8206 (mttt) cc_final: 0.7974 (mtmt) REVERT: D 76 LYS cc_start: 0.8308 (tttt) cc_final: 0.8058 (tptt) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.5373 time to fit residues: 68.9038 Evaluate side-chains 97 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 193 ASP 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 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6684 Z= 0.252 Angle : 0.550 6.107 9050 Z= 0.271 Chirality : 0.036 0.145 1074 Planarity : 0.004 0.051 1130 Dihedral : 8.420 154.217 940 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 10.15 % Favored : 88.09 % 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: 2.12 (0.30), residues: 834 helix: 2.60 (0.22), residues: 526 sheet: -1.25 (0.68), residues: 66 loop : -0.53 (0.39), residues: 242 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 0.012 0.001 PHE C 215 TYR 0.012 0.001 TYR D 250 ARG 0.007 0.000 ARG B 21 *********************** 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 110 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8190 (mttt) cc_final: 0.7910 (mtmt) REVERT: D 76 LYS cc_start: 0.8320 (tttt) cc_final: 0.8071 (tptt) outliers start: 12 outliers final: 8 residues processed: 106 average time/residue: 0.5163 time to fit residues: 69.6054 Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 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 193 ASP 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 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3920 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= 0.178 Angle : 0.531 6.232 9050 Z= 0.257 Chirality : 0.035 0.149 1074 Planarity : 0.003 0.032 1130 Dihedral : 8.403 158.582 940 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.32 % Allowed : 11.18 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.30), residues: 834 helix: 2.69 (0.22), residues: 526 sheet: -1.21 (0.68), residues: 66 loop : -0.43 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 PHE 0.010 0.001 PHE C 291 TYR 0.014 0.001 TYR A 215 ARG 0.004 0.000 ARG A 126 *********************** 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 99 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8251 (mttt) cc_final: 0.7986 (mtmt) REVERT: A 113 MET cc_start: 0.8525 (mmm) cc_final: 0.8077 (mmm) REVERT: D 76 LYS cc_start: 0.8307 (tttt) cc_final: 0.8061 (tptt) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.5109 time to fit residues: 62.6694 Evaluate side-chains 93 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 77 ASN Chi-restraints excluded: chain C residue 81 VAL 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 78 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN C 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4023 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= 0.190 Angle : 0.529 6.210 9050 Z= 0.258 Chirality : 0.035 0.146 1074 Planarity : 0.003 0.037 1130 Dihedral : 8.541 164.678 940 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.47 % Allowed : 11.32 % 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: 2.31 (0.30), residues: 834 helix: 2.72 (0.22), residues: 526 sheet: -1.16 (0.69), residues: 66 loop : -0.40 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.009 0.001 PHE B 13 TYR 0.014 0.001 TYR A 215 ARG 0.003 0.000 ARG B 21 *********************** 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 101 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8245 (mttt) cc_final: 0.7978 (mtmt) REVERT: D 76 LYS cc_start: 0.8308 (tttt) cc_final: 0.8065 (tptt) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.5143 time to fit residues: 63.9734 Evaluate side-chains 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN 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 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 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 0.027 6684 Z= 0.170 Angle : 0.524 6.280 9050 Z= 0.253 Chirality : 0.035 0.146 1074 Planarity : 0.003 0.030 1130 Dihedral : 8.816 176.002 940 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.03 % Allowed : 11.18 % 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: 2.48 (0.30), residues: 834 helix: 2.85 (0.22), residues: 526 sheet: -1.12 (0.69), residues: 66 loop : -0.29 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.009 0.001 PHE B 13 TYR 0.013 0.001 TYR A 215 ARG 0.005 0.000 ARG A 103 *********************** 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 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8304 (tttt) cc_final: 0.8074 (tptt) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.5043 time to fit residues: 57.7461 Evaluate side-chains 86 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN 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 75 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.0070 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6684 Z= 0.161 Angle : 0.517 6.196 9050 Z= 0.250 Chirality : 0.035 0.146 1074 Planarity : 0.003 0.059 1130 Dihedral : 8.923 177.570 940 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.18 % Allowed : 11.32 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 834 helix: 2.94 (0.22), residues: 526 sheet: -1.09 (0.70), residues: 66 loop : -0.26 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.005 0.001 HIS D 323 PHE 0.009 0.001 PHE B 13 TYR 0.012 0.001 TYR D 250 ARG 0.010 0.000 ARG B 21 *********************** 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 92 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8291 (tttt) cc_final: 0.8079 (tptt) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.5046 time to fit residues: 58.9559 Evaluate side-chains 90 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN 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 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 37 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6684 Z= 0.255 Angle : 0.552 6.049 9050 Z= 0.271 Chirality : 0.036 0.177 1074 Planarity : 0.003 0.051 1130 Dihedral : 8.920 179.014 940 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.18 % Allowed : 11.32 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.30), residues: 834 helix: 2.85 (0.22), residues: 526 sheet: -1.20 (0.69), residues: 66 loop : -0.30 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.005 0.001 HIS C 323 PHE 0.013 0.001 PHE B 13 TYR 0.012 0.001 TYR C 250 ARG 0.008 0.000 ARG B 21 ********************** 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 fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8247 (mttt) cc_final: 0.7977 (mtmt) REVERT: D 76 LYS cc_start: 0.8354 (tttt) cc_final: 0.8153 (tptt) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.5033 time to fit residues: 60.7383 Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN 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 65 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 61 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.123974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105508 restraints weight = 27857.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109975 restraints weight = 14071.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112957 restraints weight = 8719.301| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6684 Z= 0.163 Angle : 0.521 6.204 9050 Z= 0.252 Chirality : 0.035 0.146 1074 Planarity : 0.003 0.054 1130 Dihedral : 8.762 176.865 940 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 2.69 (0.30), residues: 834 helix: 3.02 (0.22), residues: 526 sheet: -1.13 (0.69), residues: 66 loop : -0.20 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.005 0.001 HIS A 97 PHE 0.009 0.001 PHE B 13 TYR 0.012 0.001 TYR A 215 ARG 0.008 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3116.69 seconds wall clock time: 54 minutes 45.42 seconds (3285.42 seconds total)