Starting phenix.real_space_refine on Mon Mar 11 09:00:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej7_31154/03_2024/7ej7_31154_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej7_31154/03_2024/7ej7_31154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej7_31154/03_2024/7ej7_31154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej7_31154/03_2024/7ej7_31154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej7_31154/03_2024/7ej7_31154_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej7_31154/03_2024/7ej7_31154_trim_updated.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4764 2.51 5 N 1371 2.21 5 O 1569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C GLU 319": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.73, per 1000 atoms: 0.61 Number of scatterers: 7773 At special positions: 0 Unit cell: (84.05, 96.35, 111.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 27 15.00 Mg 3 11.99 O 1569 8.00 N 1371 7.00 C 4764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 3 sheets defined 39.9% alpha, 14.6% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'B' and resid 21 through 24 removed outlier: 3.789A pdb=" N ASN B 24 " --> pdb=" O GLU B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 44 through 47 No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.997A pdb=" N LYS B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.733A pdb=" N GLN B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.709A pdb=" N VAL B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 232 through 252 removed outlier: 3.597A pdb=" N LYS B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.540A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 24 removed outlier: 3.790A pdb=" N ASN A 24 " --> pdb=" O GLU A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.999A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.733A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.710A pdb=" N VAL A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.597A pdb=" N LYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.539A pdb=" N ALA A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.789A pdb=" N ASN C 24 " --> pdb=" O GLU C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 44 through 47 No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.997A pdb=" N LYS C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.734A pdb=" N GLN C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 191 through 206 removed outlier: 3.710A pdb=" N VAL C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 232 through 252 removed outlier: 3.596A pdb=" N LYS C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.540A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.903A pdb=" N GLY B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG B 294 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 121 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS B 150 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 213 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 152 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL B 215 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 154 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 328 through 330 removed outlier: 3.901A pdb=" N GLY A 328 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG A 294 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 121 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS A 150 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 213 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 152 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL A 215 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 154 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.902A pdb=" N GLY C 328 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG C 294 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY C 121 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS C 150 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 213 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 152 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL C 215 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 154 " --> pdb=" O VAL C 215 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1293 1.30 - 1.42: 1934 1.42 - 1.55: 4576 1.55 - 1.68: 49 1.68 - 1.80: 60 Bond restraints: 7912 Sorted by residual: bond pdb=" C4 ATP C 402 " pdb=" C5 ATP C 402 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP C 402 " pdb=" C6 ATP C 402 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 ... (remaining 7907 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.68: 269 106.68 - 114.21: 4715 114.21 - 121.73: 3982 121.73 - 129.26: 1745 129.26 - 136.79: 33 Bond angle restraints: 10744 Sorted by residual: angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 118.71 18.12 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 118.74 18.09 1.00e+00 1.00e+00 3.27e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.74 16.13 1.00e+00 1.00e+00 2.60e+02 ... (remaining 10739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4104 16.75 - 33.50: 516 33.50 - 50.25: 155 50.25 - 67.01: 40 67.01 - 83.76: 33 Dihedral angle restraints: 4848 sinusoidal: 2160 harmonic: 2688 Sorted by residual: dihedral pdb=" CA ASN B 28 " pdb=" C ASN B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta harmonic sigma weight residual 180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN C 28 " pdb=" C ASN C 28 " pdb=" N ALA C 29 " pdb=" CA ALA C 29 " ideal model delta harmonic sigma weight residual -180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN A 28 " pdb=" C ASN A 28 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 843 0.037 - 0.074: 267 0.074 - 0.111: 78 0.111 - 0.147: 24 0.147 - 0.184: 6 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CA ASP A 216 " pdb=" N ASP A 216 " pdb=" C ASP A 216 " pdb=" CB ASP A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA ASP C 216 " pdb=" N ASP C 216 " pdb=" C ASP C 216 " pdb=" CB ASP C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ASP B 216 " pdb=" N ASP B 216 " pdb=" C ASP B 216 " pdb=" CB ASP B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1215 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 315 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C MET C 315 " 0.049 2.00e-02 2.50e+03 pdb=" O MET C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO C 316 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 315 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C MET A 315 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 315 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 316 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 315 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C MET B 315 " 0.049 2.00e-02 2.50e+03 pdb=" O MET B 315 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO B 316 " -0.016 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 78 2.47 - 3.08: 6340 3.08 - 3.68: 11359 3.68 - 4.29: 17711 4.29 - 4.90: 29034 Nonbonded interactions: 64522 Sorted by model distance: nonbonded pdb=" O PRO B 316 " pdb=" O2' ATP B 602 " model vdw 1.860 2.440 nonbonded pdb=" O PRO C 316 " pdb=" O2' ATP C 401 " model vdw 1.901 2.440 nonbonded pdb=" O2G ATP C 402 " pdb="MG MG C 403 " model vdw 1.913 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP C 401 " model vdw 1.913 2.170 nonbonded pdb=" O2G ATP B 602 " pdb="MG MG A 601 " model vdw 1.913 2.170 ... (remaining 64517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 334) selection = (chain 'B' and resid 16 through 334) selection = (chain 'C' and resid 16 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.010 Extract box with map and model: 9.520 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.080 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.006 0.074 7912 Z= 0.380 Angle : 0.915 18.124 10744 Z= 0.680 Chirality : 0.043 0.184 1218 Planarity : 0.004 0.044 1323 Dihedral : 18.099 83.758 3132 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 43.57 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.83 % Favored : 88.22 % Rotamer: Outliers : 1.75 % Allowed : 4.64 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -4.75 (0.22), residues: 942 helix: -3.33 (0.19), residues: 381 sheet: -0.20 (0.45), residues: 150 loop : -4.17 (0.21), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 193 PHE 0.007 0.001 PHE C 160 TYR 0.006 0.001 TYR B 41 ARG 0.003 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: B 24 ASN cc_start: 0.8704 (p0) cc_final: 0.8486 (p0) REVERT: B 61 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6156 (m) REVERT: A 61 SER cc_start: 0.6980 (OUTLIER) cc_final: 0.6729 (m) REVERT: C 61 SER cc_start: 0.6506 (OUTLIER) cc_final: 0.6167 (m) outliers start: 14 outliers final: 2 residues processed: 111 average time/residue: 0.2340 time to fit residues: 34.2665 Evaluate side-chains 68 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN B 182 ASN B 236 GLN A 182 ASN A 236 GLN C 44 ASN C 182 ASN C 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7912 Z= 0.195 Angle : 0.626 8.562 10744 Z= 0.325 Chirality : 0.045 0.144 1218 Planarity : 0.004 0.030 1323 Dihedral : 17.212 89.746 1349 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.30 % Favored : 89.07 % Rotamer: Outliers : 2.51 % Allowed : 11.40 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -3.05 (0.25), residues: 942 helix: -1.56 (0.24), residues: 417 sheet: 1.35 (0.47), residues: 144 loop : -4.02 (0.22), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 289 PHE 0.011 0.001 PHE A 160 TYR 0.013 0.001 TYR C 41 ARG 0.003 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 272 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6166 (mp) REVERT: A 89 ILE cc_start: 0.9132 (tt) cc_final: 0.8875 (mt) REVERT: C 44 ASN cc_start: 0.8983 (m-40) cc_final: 0.8721 (m110) outliers start: 20 outliers final: 11 residues processed: 112 average time/residue: 0.2262 time to fit residues: 33.5711 Evaluate side-chains 74 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7912 Z= 0.306 Angle : 0.610 7.773 10744 Z= 0.322 Chirality : 0.046 0.155 1218 Planarity : 0.004 0.031 1323 Dihedral : 17.081 89.985 1347 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.87 % Favored : 89.60 % Rotamer: Outliers : 2.63 % Allowed : 15.04 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -2.10 (0.26), residues: 942 helix: -0.56 (0.26), residues: 402 sheet: 1.48 (0.45), residues: 144 loop : -3.55 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 285 PHE 0.010 0.001 PHE B 120 TYR 0.013 0.001 TYR C 41 ARG 0.004 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6162 (mp) outliers start: 21 outliers final: 16 residues processed: 80 average time/residue: 0.2169 time to fit residues: 23.7322 Evaluate side-chains 70 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 56 optimal weight: 0.0000 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS C 44 ASN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7912 Z= 0.352 Angle : 0.611 7.540 10744 Z= 0.323 Chirality : 0.046 0.143 1218 Planarity : 0.004 0.034 1323 Dihedral : 16.844 84.342 1346 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.51 % Favored : 88.96 % Rotamer: Outliers : 3.88 % Allowed : 16.29 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.27), residues: 942 helix: -0.23 (0.26), residues: 423 sheet: 1.26 (0.44), residues: 150 loop : -3.48 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 285 PHE 0.012 0.001 PHE B 120 TYR 0.011 0.001 TYR C 41 ARG 0.003 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 60 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6262 (mp) REVERT: A 41 TYR cc_start: 0.7697 (m-80) cc_final: 0.7221 (m-10) REVERT: C 318 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7582 (mttt) outliers start: 31 outliers final: 17 residues processed: 85 average time/residue: 0.2293 time to fit residues: 26.1926 Evaluate side-chains 77 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN C 44 ASN C 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7912 Z= 0.370 Angle : 0.627 7.568 10744 Z= 0.331 Chirality : 0.046 0.143 1218 Planarity : 0.004 0.035 1323 Dihedral : 16.776 81.509 1346 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.30 % Favored : 89.17 % Rotamer: Outliers : 4.01 % Allowed : 16.29 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.27), residues: 942 helix: -0.11 (0.26), residues: 423 sheet: 1.21 (0.44), residues: 156 loop : -3.28 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 242 PHE 0.012 0.001 PHE B 120 TYR 0.010 0.001 TYR C 41 ARG 0.003 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 58 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7680 (mtmt) REVERT: A 41 TYR cc_start: 0.7659 (m-80) cc_final: 0.7225 (m-10) REVERT: C 318 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7548 (mttt) outliers start: 32 outliers final: 21 residues processed: 86 average time/residue: 0.2523 time to fit residues: 28.6509 Evaluate side-chains 75 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN B 242 HIS A 242 HIS C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7912 Z= 0.153 Angle : 0.540 5.422 10744 Z= 0.286 Chirality : 0.042 0.131 1218 Planarity : 0.003 0.036 1323 Dihedral : 16.518 85.255 1346 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.55 % Favored : 89.92 % Rotamer: Outliers : 2.76 % Allowed : 17.92 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 942 helix: 0.37 (0.27), residues: 414 sheet: 1.88 (0.44), residues: 144 loop : -2.87 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 193 PHE 0.007 0.001 PHE B 120 TYR 0.009 0.001 TYR C 41 ARG 0.002 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7288 (mtmt) REVERT: A 34 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8148 (mtmm) REVERT: A 41 TYR cc_start: 0.7519 (m-80) cc_final: 0.7066 (m-10) REVERT: C 34 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8258 (mtmm) REVERT: C 240 ASN cc_start: 0.9227 (t0) cc_final: 0.8947 (t0) REVERT: C 318 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7389 (mttt) outliers start: 22 outliers final: 16 residues processed: 95 average time/residue: 0.2611 time to fit residues: 31.8255 Evaluate side-chains 82 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN B 242 HIS A 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7912 Z= 0.161 Angle : 0.543 5.657 10744 Z= 0.286 Chirality : 0.043 0.233 1218 Planarity : 0.003 0.035 1323 Dihedral : 16.469 84.097 1346 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.13 % Favored : 90.34 % Rotamer: Outliers : 2.88 % Allowed : 18.42 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 942 helix: 0.51 (0.27), residues: 414 sheet: 1.92 (0.43), residues: 150 loop : -2.87 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 285 PHE 0.009 0.001 PHE C 123 TYR 0.013 0.001 TYR B 185 ARG 0.003 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7269 (mtmt) REVERT: A 34 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8120 (mtmm) REVERT: A 41 TYR cc_start: 0.7537 (m-80) cc_final: 0.7082 (m-10) REVERT: A 144 MET cc_start: 0.7493 (mtm) cc_final: 0.7077 (mtm) REVERT: C 34 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8255 (mtmm) REVERT: C 240 ASN cc_start: 0.9253 (t0) cc_final: 0.8956 (t0) REVERT: C 318 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7347 (mtmt) outliers start: 23 outliers final: 17 residues processed: 87 average time/residue: 0.2435 time to fit residues: 27.9424 Evaluate side-chains 82 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7912 Z= 0.345 Angle : 0.607 5.203 10744 Z= 0.321 Chirality : 0.046 0.249 1218 Planarity : 0.004 0.033 1323 Dihedral : 16.553 78.694 1346 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.30 % Favored : 89.17 % Rotamer: Outliers : 3.26 % Allowed : 18.42 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.29), residues: 942 helix: 0.48 (0.27), residues: 417 sheet: 1.81 (0.44), residues: 150 loop : -3.00 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 285 PHE 0.011 0.001 PHE B 120 TYR 0.011 0.001 TYR B 185 ARG 0.004 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7554 (mtmt) REVERT: A 34 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8136 (mtmm) REVERT: A 41 TYR cc_start: 0.7582 (m-80) cc_final: 0.7164 (m-10) REVERT: A 144 MET cc_start: 0.7607 (mtm) cc_final: 0.7233 (mtm) REVERT: C 34 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8274 (mtmm) REVERT: C 318 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7452 (mttt) outliers start: 26 outliers final: 19 residues processed: 84 average time/residue: 0.2442 time to fit residues: 27.8780 Evaluate side-chains 79 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 88 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS C 241 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7912 Z= 0.148 Angle : 0.543 6.794 10744 Z= 0.286 Chirality : 0.043 0.185 1218 Planarity : 0.003 0.034 1323 Dihedral : 16.422 82.941 1346 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.45 % Favored : 90.02 % Rotamer: Outliers : 3.01 % Allowed : 19.05 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 942 helix: 0.61 (0.27), residues: 414 sheet: 2.10 (0.43), residues: 144 loop : -2.74 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 289 PHE 0.007 0.001 PHE C 120 TYR 0.011 0.001 TYR B 185 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7227 (mtmt) REVERT: A 34 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8125 (mtmm) REVERT: A 41 TYR cc_start: 0.7348 (m-80) cc_final: 0.6926 (m-10) REVERT: A 144 MET cc_start: 0.7444 (mtm) cc_final: 0.7147 (mtm) REVERT: C 34 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8245 (mtmm) REVERT: C 240 ASN cc_start: 0.9234 (t0) cc_final: 0.8963 (t0) REVERT: C 318 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7328 (mtmt) outliers start: 24 outliers final: 17 residues processed: 90 average time/residue: 0.2658 time to fit residues: 31.0054 Evaluate side-chains 85 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS A 242 HIS C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7912 Z= 0.147 Angle : 0.541 6.110 10744 Z= 0.284 Chirality : 0.042 0.171 1218 Planarity : 0.003 0.035 1323 Dihedral : 16.398 84.473 1346 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.45 % Rotamer: Outliers : 2.01 % Allowed : 19.80 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 942 helix: 0.70 (0.27), residues: 414 sheet: 2.16 (0.43), residues: 144 loop : -2.71 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 285 PHE 0.009 0.001 PHE C 123 TYR 0.010 0.001 TYR B 185 ARG 0.002 0.000 ARG B 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8157 (mtmm) REVERT: C 318 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7360 (mtmt) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.2423 time to fit residues: 27.3451 Evaluate side-chains 75 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 318 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.077024 restraints weight = 14100.933| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.53 r_work: 0.2765 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7912 Z= 0.252 Angle : 0.583 7.569 10744 Z= 0.306 Chirality : 0.044 0.183 1218 Planarity : 0.004 0.033 1323 Dihedral : 16.390 80.878 1346 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.66 % Favored : 89.81 % Rotamer: Outliers : 2.01 % Allowed : 19.92 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.29), residues: 942 helix: 0.70 (0.27), residues: 414 sheet: 1.95 (0.43), residues: 150 loop : -2.81 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 285 PHE 0.010 0.001 PHE B 120 TYR 0.009 0.001 TYR B 185 ARG 0.003 0.000 ARG C 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.16 seconds wall clock time: 33 minutes 16.64 seconds (1996.64 seconds total)