Starting phenix.real_space_refine on Sat Apr 6 13:40:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/04_2024/7xp6_33366_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/04_2024/7xp6_33366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/04_2024/7xp6_33366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/04_2024/7xp6_33366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/04_2024/7xp6_33366_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/04_2024/7xp6_33366_updated.pdb" } resolution = 3.01 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= 0.023 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5322 2.51 5 N 1436 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8336 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1964 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 981 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2330 Unusual residues: {'SY9': 1} Classifications: {'peptide': 283, 'undetermined': 1} Link IDs: {'PTRANS': 8, 'TRANS': 274, None: 1} Not linked: pdbres="VAL R 301 " pdbres="SY9 R 501 " Chain breaks: 1 Time building chain proxies: 5.08, per 1000 atoms: 0.61 Number of scatterers: 8336 At special positions: 0 Unit cell: (79.04, 101.92, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1531 8.00 N 1436 7.00 C 5322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.04 Simple disulfide: pdb=" SG CYS N 100 " - pdb=" SG CYS N 108 " distance=2.03 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 41.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 35 Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.656A pdb=" N LEU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 118 through 132 removed outlier: 4.184A pdb=" N GLN A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 163 through 166 No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 187 through 206 Processing helix chain 'A' and resid 223 through 246 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.578A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 30 through 32 No H-bonds generated for 'chain 'N' and resid 30 through 32' Processing helix chain 'N' and resid 63 through 65 No H-bonds generated for 'chain 'N' and resid 63 through 65' Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'R' and resid 4 through 38 Processing helix chain 'R' and resid 43 through 70 Processing helix chain 'R' and resid 77 through 110 Processing helix chain 'R' and resid 116 through 123 Processing helix chain 'R' and resid 125 through 153 Proline residue: R 136 - end of helix Processing helix chain 'R' and resid 174 through 212 removed outlier: 3.568A pdb=" N LEU R 182 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Proline residue: R 187 - end of helix removed outlier: 3.680A pdb=" N LEU R 211 " --> pdb=" O LYS R 207 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS R 212 " --> pdb=" O LYS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 253 Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.745A pdb=" N PHE R 263 " --> pdb=" O PRO R 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA R 268 " --> pdb=" O CYS R 264 " (cutoff:3.500A) Proline residue: R 272 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 284 through 300 Processing sheet with id= A, first strand: chain 'A' and resid 214 through 218 removed outlier: 7.292A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 108 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 89 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY A 43 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.186A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.678A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.902A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.638A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.450A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.675A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.767A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 123 through 125 removed outlier: 6.313A pdb=" N ARG N 39 " --> pdb=" O TRP N 48 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TRP N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2696 1.34 - 1.46: 1999 1.46 - 1.58: 3757 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8518 Sorted by residual: bond pdb=" CAV SY9 R 501 " pdb=" NAY SY9 R 501 " ideal model delta sigma weight residual 1.454 1.501 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CAG SY9 R 501 " pdb=" CAV SY9 R 501 " ideal model delta sigma weight residual 1.578 1.544 0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" CAX SY9 R 501 " pdb=" NAY SY9 R 501 " ideal model delta sigma weight residual 1.449 1.482 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" N THR N 112 " pdb=" CA THR N 112 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.50e+00 bond pdb=" CAM SY9 R 501 " pdb=" OAO SY9 R 501 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 8513 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.54: 180 106.54 - 113.41: 4709 113.41 - 120.27: 2954 120.27 - 127.14: 3612 127.14 - 134.01: 94 Bond angle restraints: 11549 Sorted by residual: angle pdb=" CA PRO R 187 " pdb=" N PRO R 187 " pdb=" CD PRO R 187 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C GLY A 159 " pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CB MET R 247 " pdb=" CG MET R 247 " pdb=" SD MET R 247 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " pdb=" CG ARG A 172 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 angle pdb=" C ASP B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 126.63 -3.89 1.44e+00 4.82e-01 7.29e+00 ... (remaining 11544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 5019 34.38 - 68.76: 74 68.76 - 103.14: 2 103.14 - 137.51: 3 137.51 - 171.89: 1 Dihedral angle restraints: 5099 sinusoidal: 2045 harmonic: 3054 Sorted by residual: dihedral pdb=" CAM SY9 R 501 " pdb=" CAP SY9 R 501 " pdb=" OAO SY9 R 501 " pdb=" CAQ SY9 R 501 " ideal model delta sinusoidal sigma weight residual -84.84 87.05 -171.89 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CAR SY9 R 501 " pdb=" CAP SY9 R 501 " pdb=" CAQ SY9 R 501 " pdb=" OAO SY9 R 501 " ideal model delta sinusoidal sigma weight residual 65.89 -56.55 122.44 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1073 0.051 - 0.101: 192 0.101 - 0.152: 42 0.152 - 0.203: 3 0.203 - 0.253: 2 Chirality restraints: 1312 Sorted by residual: chirality pdb=" NAY SY9 R 501 " pdb=" CAS SY9 R 501 " pdb=" CAV SY9 R 501 " pdb=" CAX SY9 R 501 " both_signs ideal model delta sigma weight residual False -2.12 -2.38 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CAK SY9 R 501 " pdb=" CAG SY9 R 501 " pdb=" CAN SY9 R 501 " pdb=" NAH SY9 R 501 " both_signs ideal model delta sigma weight residual False 2.54 2.77 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1309 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 R 501 " 0.233 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CAI SY9 R 501 " -0.048 2.00e-02 2.50e+03 pdb=" CAK SY9 R 501 " -0.105 2.00e-02 2.50e+03 pdb=" CAL SY9 R 501 " 0.202 2.00e-02 2.50e+03 pdb=" NAH SY9 R 501 " -0.189 2.00e-02 2.50e+03 pdb=" OAJ SY9 R 501 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 186 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO R 187 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 271 " -0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO R 272 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO R 272 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 272 " -0.040 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 7974 3.22 - 3.78: 12978 3.78 - 4.34: 17264 4.34 - 4.90: 29100 Nonbonded interactions: 67437 Sorted by model distance: nonbonded pdb=" OH TYR A 173 " pdb=" OD2 ASP A 198 " model vdw 2.100 2.440 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.183 2.440 nonbonded pdb=" O ALA A 44 " pdb=" OG SER A 47 " model vdw 2.187 2.440 nonbonded pdb=" OG SER R 103 " pdb=" OG SER R 194 " model vdw 2.200 2.440 nonbonded pdb=" O TYR A 173 " pdb=" NH1 ARG A 191 " model vdw 2.202 2.520 ... (remaining 67432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.720 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: 3.830 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.003 0.052 8518 Z= 0.214 Angle : 0.593 10.023 11549 Z= 0.329 Chirality : 0.042 0.253 1312 Planarity : 0.007 0.159 1456 Dihedral : 13.311 171.893 3113 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.78 (0.26), residues: 1037 helix: 2.57 (0.23), residues: 424 sheet: 0.99 (0.34), residues: 238 loop : -0.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 99 HIS 0.005 0.001 HIS A 212 PHE 0.026 0.001 PHE R 9 TYR 0.029 0.002 TYR B 59 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 VAL cc_start: 0.8127 (t) cc_final: 0.7919 (t) REVERT: B 8 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7586 (ttt180) REVERT: B 13 GLN cc_start: 0.7979 (tp40) cc_final: 0.7088 (tp40) REVERT: B 45 MET cc_start: 0.8471 (mtp) cc_final: 0.8263 (mtp) REVERT: B 134 ARG cc_start: 0.7572 (ptp-110) cc_final: 0.7261 (ptp90) REVERT: B 264 TYR cc_start: 0.8318 (m-80) cc_final: 0.7988 (m-80) REVERT: B 317 CYS cc_start: 0.6807 (p) cc_final: 0.6541 (p) REVERT: G 19 LEU cc_start: 0.8425 (mm) cc_final: 0.8207 (mm) REVERT: N 14 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7045 (mm-40) REVERT: N 32 ASN cc_start: 0.8571 (m-40) cc_final: 0.8300 (m110) REVERT: N 53 SER cc_start: 0.8060 (t) cc_final: 0.7538 (m) REVERT: R 36 PHE cc_start: 0.7327 (t80) cc_final: 0.7029 (t80) REVERT: R 149 MET cc_start: 0.5481 (tpt) cc_final: 0.5205 (tpt) REVERT: R 181 ILE cc_start: 0.7706 (mm) cc_final: 0.7456 (mm) REVERT: R 193 ILE cc_start: 0.8154 (tp) cc_final: 0.7920 (tp) REVERT: R 222 LYS cc_start: 0.7408 (tmtt) cc_final: 0.7153 (tmtt) REVERT: R 285 LYS cc_start: 0.8465 (pptt) cc_final: 0.8195 (pptt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2757 time to fit residues: 82.1883 Evaluate side-chains 225 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 110 ASN B 119 ASN B 155 ASN R 205 HIS R 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8518 Z= 0.247 Angle : 0.525 7.616 11549 Z= 0.285 Chirality : 0.043 0.195 1312 Planarity : 0.005 0.072 1456 Dihedral : 8.194 150.611 1193 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.54 % Allowed : 8.68 % Favored : 89.78 % 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: 1.84 (0.25), residues: 1037 helix: 2.70 (0.23), residues: 437 sheet: 0.96 (0.33), residues: 232 loop : -0.43 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS A 212 PHE 0.025 0.002 PHE A 87 TYR 0.028 0.002 TYR B 59 ARG 0.007 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 243 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 VAL cc_start: 0.8187 (t) cc_final: 0.7978 (t) REVERT: A 87 PHE cc_start: 0.8039 (p90) cc_final: 0.7699 (p90) REVERT: A 226 ASN cc_start: 0.8082 (m110) cc_final: 0.7758 (m-40) REVERT: B 8 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7575 (ttt180) REVERT: B 13 GLN cc_start: 0.7998 (tp40) cc_final: 0.7100 (tp40) REVERT: B 46 ARG cc_start: 0.6895 (mtm-85) cc_final: 0.6645 (mtm-85) REVERT: B 72 SER cc_start: 0.8139 (t) cc_final: 0.7856 (t) REVERT: B 134 ARG cc_start: 0.7565 (ptp-110) cc_final: 0.7326 (ptp90) REVERT: B 246 ASP cc_start: 0.7553 (m-30) cc_final: 0.7251 (m-30) REVERT: B 317 CYS cc_start: 0.6678 (p) cc_final: 0.6464 (p) REVERT: N 14 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7174 (mm110) REVERT: N 32 ASN cc_start: 0.8621 (m-40) cc_final: 0.8412 (m110) REVERT: N 61 TYR cc_start: 0.8259 (m-80) cc_final: 0.7744 (m-80) REVERT: N 121 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7221 (mm-40) REVERT: R 149 MET cc_start: 0.5481 (tpt) cc_final: 0.5230 (tpt) REVERT: R 181 ILE cc_start: 0.7629 (mm) cc_final: 0.7392 (mm) REVERT: R 193 ILE cc_start: 0.7940 (tp) cc_final: 0.7679 (tp) REVERT: R 222 LYS cc_start: 0.7458 (tmtt) cc_final: 0.7169 (tmtt) REVERT: R 280 ILE cc_start: 0.8732 (mt) cc_final: 0.8502 (mm) REVERT: R 285 LYS cc_start: 0.8548 (pptt) cc_final: 0.8272 (pptt) outliers start: 14 outliers final: 12 residues processed: 244 average time/residue: 0.2711 time to fit residues: 84.0194 Evaluate side-chains 246 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 234 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 16 ASN B 119 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN R 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8518 Z= 0.211 Angle : 0.501 8.712 11549 Z= 0.267 Chirality : 0.041 0.184 1312 Planarity : 0.004 0.064 1456 Dihedral : 7.732 141.303 1193 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.42 % Allowed : 11.54 % Favored : 86.04 % 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: 1.84 (0.26), residues: 1037 helix: 2.75 (0.23), residues: 437 sheet: 0.76 (0.34), residues: 236 loop : -0.37 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.022 0.001 TYR B 59 ARG 0.004 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 243 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8073 (p90) cc_final: 0.7641 (p90) REVERT: A 129 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8421 (ttmm) REVERT: A 134 ASN cc_start: 0.7620 (t0) cc_final: 0.7340 (t0) REVERT: A 226 ASN cc_start: 0.8068 (m110) cc_final: 0.7734 (m-40) REVERT: B 8 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7592 (ttt180) REVERT: B 13 GLN cc_start: 0.7994 (tp40) cc_final: 0.7116 (tp40) REVERT: B 45 MET cc_start: 0.8465 (mtp) cc_final: 0.8222 (mtp) REVERT: B 134 ARG cc_start: 0.7484 (ptp-110) cc_final: 0.7271 (ptp90) REVERT: B 246 ASP cc_start: 0.7528 (m-30) cc_final: 0.7245 (m-30) REVERT: N 14 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7160 (mm110) REVERT: N 32 ASN cc_start: 0.8601 (m110) cc_final: 0.8332 (m110) REVERT: N 61 TYR cc_start: 0.8245 (m-80) cc_final: 0.7762 (m-80) REVERT: N 109 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: R 149 MET cc_start: 0.5402 (tpt) cc_final: 0.5191 (tpt) REVERT: R 181 ILE cc_start: 0.7589 (mm) cc_final: 0.7344 (mm) REVERT: R 193 ILE cc_start: 0.7899 (tp) cc_final: 0.7642 (tp) REVERT: R 222 LYS cc_start: 0.7465 (tmtt) cc_final: 0.7148 (tmtt) outliers start: 22 outliers final: 19 residues processed: 247 average time/residue: 0.2712 time to fit residues: 85.6245 Evaluate side-chains 258 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.0170 chunk 99 optimal weight: 0.0050 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN B 119 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8518 Z= 0.187 Angle : 0.495 8.169 11549 Z= 0.259 Chirality : 0.040 0.132 1312 Planarity : 0.004 0.059 1456 Dihedral : 5.596 108.219 1193 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.19 % Allowed : 12.09 % Favored : 84.73 % 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: 1.84 (0.26), residues: 1037 helix: 2.81 (0.23), residues: 437 sheet: 0.72 (0.34), residues: 229 loop : -0.41 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.017 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 239 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7876 (tp-100) REVERT: A 87 PHE cc_start: 0.8102 (p90) cc_final: 0.7650 (p90) REVERT: A 129 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8398 (ttmm) REVERT: A 134 ASN cc_start: 0.7725 (t0) cc_final: 0.7373 (t0) REVERT: A 226 ASN cc_start: 0.8044 (m110) cc_final: 0.7717 (m-40) REVERT: B 8 ARG cc_start: 0.7815 (ttt180) cc_final: 0.7579 (ttt180) REVERT: B 13 GLN cc_start: 0.7993 (tp40) cc_final: 0.7105 (tp40) REVERT: B 45 MET cc_start: 0.8475 (mtp) cc_final: 0.8220 (mtp) REVERT: B 134 ARG cc_start: 0.7491 (ptp-110) cc_final: 0.7189 (ptp90) REVERT: B 212 ASP cc_start: 0.7585 (t0) cc_final: 0.7267 (t0) REVERT: B 246 ASP cc_start: 0.7549 (m-30) cc_final: 0.7300 (m-30) REVERT: N 14 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7150 (mm110) REVERT: N 32 ASN cc_start: 0.8581 (m110) cc_final: 0.8325 (m110) REVERT: N 61 TYR cc_start: 0.8252 (m-80) cc_final: 0.7788 (m-80) REVERT: N 109 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5939 (m-80) REVERT: R 149 MET cc_start: 0.5428 (tpt) cc_final: 0.5200 (tpt) REVERT: R 193 ILE cc_start: 0.7876 (tp) cc_final: 0.7631 (tp) REVERT: R 222 LYS cc_start: 0.7403 (tmtt) cc_final: 0.7067 (tmtt) REVERT: R 247 MET cc_start: 0.6093 (mmm) cc_final: 0.5878 (mmm) outliers start: 29 outliers final: 19 residues processed: 247 average time/residue: 0.2718 time to fit residues: 85.6302 Evaluate side-chains 257 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8518 Z= 0.305 Angle : 0.535 6.977 11549 Z= 0.285 Chirality : 0.042 0.210 1312 Planarity : 0.004 0.056 1456 Dihedral : 4.359 19.904 1193 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 3.63 % Allowed : 12.86 % Favored : 83.52 % 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: 1.57 (0.26), residues: 1037 helix: 2.54 (0.23), residues: 437 sheet: 0.54 (0.33), residues: 229 loop : -0.45 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 66 HIS 0.006 0.001 HIS A 85 PHE 0.015 0.001 PHE R 188 TYR 0.019 0.002 TYR B 59 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 251 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7078 (t0) cc_final: 0.6656 (t0) REVERT: A 87 PHE cc_start: 0.8220 (p90) cc_final: 0.7657 (p90) REVERT: A 122 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7935 (tp40) REVERT: A 129 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8387 (ttmm) REVERT: A 134 ASN cc_start: 0.7868 (t0) cc_final: 0.7595 (t0) REVERT: A 169 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6575 (mm-30) REVERT: A 223 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6405 (m-30) REVERT: A 226 ASN cc_start: 0.8135 (m110) cc_final: 0.7765 (m-40) REVERT: B 8 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7568 (ttt180) REVERT: B 13 GLN cc_start: 0.8010 (tp40) cc_final: 0.7154 (tp40) REVERT: B 72 SER cc_start: 0.8080 (t) cc_final: 0.7805 (t) REVERT: B 189 SER cc_start: 0.8215 (t) cc_final: 0.7997 (t) REVERT: B 246 ASP cc_start: 0.7580 (m-30) cc_final: 0.7333 (m-30) REVERT: N 14 GLN cc_start: 0.7346 (mm-40) cc_final: 0.7117 (mm-40) REVERT: N 32 ASN cc_start: 0.8619 (m110) cc_final: 0.8342 (m110) REVERT: N 109 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: R 149 MET cc_start: 0.5499 (tpt) cc_final: 0.5268 (tpt) REVERT: R 193 ILE cc_start: 0.7939 (tp) cc_final: 0.7694 (tp) REVERT: R 222 LYS cc_start: 0.7590 (tmtt) cc_final: 0.7229 (tmtt) REVERT: R 247 MET cc_start: 0.6099 (mmm) cc_final: 0.5855 (mmm) outliers start: 33 outliers final: 23 residues processed: 258 average time/residue: 0.2723 time to fit residues: 90.5058 Evaluate side-chains 270 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 88 ASN B 119 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8518 Z= 0.171 Angle : 0.485 6.764 11549 Z= 0.257 Chirality : 0.040 0.150 1312 Planarity : 0.004 0.052 1456 Dihedral : 4.076 20.874 1193 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 2.97 % Allowed : 14.73 % Favored : 82.31 % 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: 1.73 (0.26), residues: 1037 helix: 2.70 (0.23), residues: 437 sheet: 0.61 (0.33), residues: 232 loop : -0.39 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 66 HIS 0.004 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.014 0.001 TYR R 241 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 245 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8195 (p90) cc_final: 0.7607 (p90) REVERT: A 129 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8382 (ttmm) REVERT: A 134 ASN cc_start: 0.7813 (t0) cc_final: 0.7524 (t0) REVERT: A 169 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6495 (mm-30) REVERT: A 223 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6543 (m-30) REVERT: A 226 ASN cc_start: 0.8066 (m110) cc_final: 0.7729 (m-40) REVERT: A 236 ASP cc_start: 0.7536 (t0) cc_final: 0.7240 (t70) REVERT: B 8 ARG cc_start: 0.7825 (ttt180) cc_final: 0.7559 (ttt180) REVERT: B 13 GLN cc_start: 0.7987 (tp40) cc_final: 0.7131 (tp40) REVERT: B 45 MET cc_start: 0.8467 (mtp) cc_final: 0.8210 (mtp) REVERT: B 189 SER cc_start: 0.8138 (t) cc_final: 0.7903 (t) REVERT: B 246 ASP cc_start: 0.7560 (m-30) cc_final: 0.7324 (m-30) REVERT: B 317 CYS cc_start: 0.6812 (p) cc_final: 0.6532 (p) REVERT: G 41 CYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6590 (p) REVERT: N 14 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7095 (mm-40) REVERT: N 61 TYR cc_start: 0.8150 (m-80) cc_final: 0.7681 (m-80) REVERT: N 109 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.5880 (m-80) REVERT: R 149 MET cc_start: 0.5423 (tpt) cc_final: 0.5152 (tpt) REVERT: R 193 ILE cc_start: 0.7904 (tp) cc_final: 0.7665 (tp) REVERT: R 222 LYS cc_start: 0.7390 (tmtt) cc_final: 0.7043 (tmtt) REVERT: R 247 MET cc_start: 0.6076 (mmm) cc_final: 0.5797 (mmm) outliers start: 27 outliers final: 18 residues processed: 253 average time/residue: 0.2652 time to fit residues: 85.8169 Evaluate side-chains 262 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8518 Z= 0.206 Angle : 0.494 6.664 11549 Z= 0.261 Chirality : 0.040 0.178 1312 Planarity : 0.004 0.049 1456 Dihedral : 4.068 21.882 1193 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.97 % Allowed : 15.60 % Favored : 81.43 % 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: 1.69 (0.26), residues: 1037 helix: 2.67 (0.23), residues: 437 sheet: 0.57 (0.33), residues: 227 loop : -0.39 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 300 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8222 (p90) cc_final: 0.7593 (p90) REVERT: A 106 VAL cc_start: 0.8047 (t) cc_final: 0.7837 (m) REVERT: A 129 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8369 (ttmm) REVERT: A 134 ASN cc_start: 0.7848 (t0) cc_final: 0.7540 (t0) REVERT: A 169 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6502 (mm-30) REVERT: A 198 ASP cc_start: 0.6931 (t0) cc_final: 0.6533 (t0) REVERT: A 223 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6534 (m-30) REVERT: A 226 ASN cc_start: 0.8079 (m110) cc_final: 0.7724 (m-40) REVERT: B 8 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7533 (ttt180) REVERT: B 13 GLN cc_start: 0.7994 (tp40) cc_final: 0.7138 (tp40) REVERT: B 45 MET cc_start: 0.8481 (mtp) cc_final: 0.8227 (mtp) REVERT: B 189 SER cc_start: 0.8128 (t) cc_final: 0.7888 (t) REVERT: B 246 ASP cc_start: 0.7576 (m-30) cc_final: 0.7335 (m-30) REVERT: B 317 CYS cc_start: 0.6840 (p) cc_final: 0.6534 (p) REVERT: G 41 CYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6601 (p) REVERT: N 14 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7147 (mm-40) REVERT: N 61 TYR cc_start: 0.8260 (m-80) cc_final: 0.7786 (m-80) REVERT: N 109 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: R 149 MET cc_start: 0.5429 (tpt) cc_final: 0.5163 (tpt) REVERT: R 193 ILE cc_start: 0.7912 (tp) cc_final: 0.7672 (tp) REVERT: R 222 LYS cc_start: 0.7444 (tmtt) cc_final: 0.7098 (tmtt) REVERT: R 247 MET cc_start: 0.6065 (mmm) cc_final: 0.5767 (mmm) outliers start: 27 outliers final: 22 residues processed: 244 average time/residue: 0.2739 time to fit residues: 85.0545 Evaluate side-chains 262 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8518 Z= 0.247 Angle : 0.513 6.840 11549 Z= 0.272 Chirality : 0.041 0.172 1312 Planarity : 0.004 0.047 1456 Dihedral : 4.168 23.026 1193 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 2.86 % Allowed : 16.26 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1037 helix: 2.54 (0.23), residues: 437 sheet: 0.42 (0.33), residues: 229 loop : -0.40 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 300 HIS 0.005 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7050 (t0) cc_final: 0.6648 (t0) REVERT: A 87 PHE cc_start: 0.8239 (p90) cc_final: 0.7619 (p90) REVERT: A 129 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8364 (ttmm) REVERT: A 134 ASN cc_start: 0.7900 (t0) cc_final: 0.7578 (t0) REVERT: A 140 ILE cc_start: 0.8392 (mm) cc_final: 0.8090 (tt) REVERT: A 169 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6690 (mm-30) REVERT: A 198 ASP cc_start: 0.6940 (t0) cc_final: 0.6584 (t0) REVERT: A 223 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: A 226 ASN cc_start: 0.8105 (m110) cc_final: 0.7746 (m-40) REVERT: B 8 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7525 (ttt180) REVERT: B 13 GLN cc_start: 0.7998 (tp40) cc_final: 0.7263 (tp40) REVERT: B 45 MET cc_start: 0.8488 (mtp) cc_final: 0.8231 (mtp) REVERT: B 72 SER cc_start: 0.8085 (t) cc_final: 0.7827 (t) REVERT: B 189 SER cc_start: 0.8146 (t) cc_final: 0.7908 (t) REVERT: B 246 ASP cc_start: 0.7589 (m-30) cc_final: 0.7335 (m-30) REVERT: B 317 CYS cc_start: 0.6841 (p) cc_final: 0.6520 (p) REVERT: G 41 CYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6617 (p) REVERT: N 14 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7119 (mm-40) REVERT: N 61 TYR cc_start: 0.8174 (m-80) cc_final: 0.7737 (m-80) REVERT: N 109 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: R 149 MET cc_start: 0.5461 (tpt) cc_final: 0.5184 (tpt) REVERT: R 193 ILE cc_start: 0.7917 (tp) cc_final: 0.7683 (tp) REVERT: R 222 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7180 (tmtt) REVERT: R 247 MET cc_start: 0.6057 (mmm) cc_final: 0.5768 (mmm) outliers start: 26 outliers final: 22 residues processed: 249 average time/residue: 0.2614 time to fit residues: 82.9156 Evaluate side-chains 267 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 95 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8518 Z= 0.178 Angle : 0.495 6.756 11549 Z= 0.261 Chirality : 0.040 0.160 1312 Planarity : 0.004 0.047 1456 Dihedral : 4.026 20.541 1193 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.64 % Allowed : 17.36 % Favored : 80.00 % 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: 1.65 (0.26), residues: 1037 helix: 2.63 (0.24), residues: 437 sheet: 0.46 (0.33), residues: 232 loop : -0.36 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.013 0.001 TYR R 241 ARG 0.005 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 237 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8664 (t) cc_final: 0.8449 (m) REVERT: A 87 PHE cc_start: 0.8229 (p90) cc_final: 0.7577 (p90) REVERT: A 106 VAL cc_start: 0.7980 (t) cc_final: 0.7777 (m) REVERT: A 129 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8341 (ttmm) REVERT: A 169 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6670 (mm-30) REVERT: A 198 ASP cc_start: 0.6895 (t0) cc_final: 0.6542 (t0) REVERT: A 223 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: A 236 ASP cc_start: 0.7524 (t0) cc_final: 0.7090 (t0) REVERT: A 248 LEU cc_start: 0.8279 (mp) cc_final: 0.7944 (mp) REVERT: B 8 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7537 (ttt180) REVERT: B 13 GLN cc_start: 0.7983 (tp40) cc_final: 0.7283 (tp40) REVERT: B 45 MET cc_start: 0.8473 (mtp) cc_final: 0.8214 (mtp) REVERT: B 189 SER cc_start: 0.8136 (t) cc_final: 0.7894 (t) REVERT: B 246 ASP cc_start: 0.7572 (m-30) cc_final: 0.7322 (m-30) REVERT: B 317 CYS cc_start: 0.6840 (p) cc_final: 0.6516 (p) REVERT: G 41 CYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6606 (p) REVERT: N 14 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7145 (mm-40) REVERT: N 61 TYR cc_start: 0.8171 (m-80) cc_final: 0.7687 (m-80) REVERT: R 106 TYR cc_start: 0.8086 (m-10) cc_final: 0.7852 (m-10) REVERT: R 149 MET cc_start: 0.5405 (tpt) cc_final: 0.5085 (tpt) REVERT: R 193 ILE cc_start: 0.7895 (tp) cc_final: 0.7669 (tp) REVERT: R 222 LYS cc_start: 0.7436 (tmtt) cc_final: 0.7068 (tmtt) REVERT: R 247 MET cc_start: 0.6032 (mmm) cc_final: 0.5758 (mmm) outliers start: 24 outliers final: 19 residues processed: 244 average time/residue: 0.2778 time to fit residues: 86.1859 Evaluate side-chains 252 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 231 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8518 Z= 0.185 Angle : 0.504 6.653 11549 Z= 0.265 Chirality : 0.040 0.163 1312 Planarity : 0.004 0.047 1456 Dihedral : 4.010 22.898 1193 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.42 % Allowed : 17.80 % Favored : 79.78 % 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: 1.64 (0.26), residues: 1037 helix: 2.66 (0.24), residues: 437 sheet: 0.41 (0.33), residues: 232 loop : -0.38 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.015 0.001 TYR B 59 ARG 0.005 0.000 ARG A 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8698 (t) cc_final: 0.8463 (m) REVERT: A 87 PHE cc_start: 0.8225 (p90) cc_final: 0.7595 (p90) REVERT: A 129 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8361 (ttmm) REVERT: A 198 ASP cc_start: 0.6891 (t0) cc_final: 0.6532 (t0) REVERT: A 223 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6537 (m-30) REVERT: A 236 ASP cc_start: 0.7524 (t0) cc_final: 0.7094 (t0) REVERT: B 8 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7525 (ttt180) REVERT: B 13 GLN cc_start: 0.7977 (tp40) cc_final: 0.7282 (tp40) REVERT: B 45 MET cc_start: 0.8475 (mtp) cc_final: 0.8217 (mtp) REVERT: B 189 SER cc_start: 0.8127 (t) cc_final: 0.7879 (t) REVERT: B 246 ASP cc_start: 0.7579 (m-30) cc_final: 0.7333 (m-30) REVERT: B 317 CYS cc_start: 0.6840 (p) cc_final: 0.6509 (p) REVERT: G 41 CYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6616 (p) REVERT: N 14 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7144 (mm-40) REVERT: N 61 TYR cc_start: 0.8280 (m-80) cc_final: 0.7742 (m-80) REVERT: R 106 TYR cc_start: 0.8081 (m-10) cc_final: 0.7744 (m-10) REVERT: R 149 MET cc_start: 0.5371 (tpt) cc_final: 0.5057 (tpt) REVERT: R 193 ILE cc_start: 0.7897 (tp) cc_final: 0.7676 (tp) REVERT: R 222 LYS cc_start: 0.7416 (tmtt) cc_final: 0.7050 (tmtt) REVERT: R 247 MET cc_start: 0.6036 (mmm) cc_final: 0.5764 (mmm) outliers start: 22 outliers final: 18 residues processed: 242 average time/residue: 0.2832 time to fit residues: 86.7870 Evaluate side-chains 249 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 299 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 155 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126476 restraints weight = 12787.541| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.34 r_work: 0.3493 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8518 Z= 0.209 Angle : 0.510 6.855 11549 Z= 0.269 Chirality : 0.041 0.159 1312 Planarity : 0.004 0.047 1456 Dihedral : 4.038 22.725 1193 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.20 % Allowed : 18.68 % Favored : 79.12 % 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: 1.59 (0.26), residues: 1037 helix: 2.64 (0.24), residues: 436 sheet: 0.42 (0.33), residues: 227 loop : -0.44 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 300 HIS 0.005 0.001 HIS A 212 PHE 0.021 0.001 PHE A 231 TYR 0.011 0.001 TYR R 241 ARG 0.005 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.62 seconds wall clock time: 44 minutes 21.51 seconds (2661.51 seconds total)