Starting phenix.real_space_refine on Fri Jul 19 16:14:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/07_2024/7xp6_33366.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/07_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_33366/07_2024/7xp6_33366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/07_2024/7xp6_33366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/07_2024/7xp6_33366.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp6_33366/07_2024/7xp6_33366.cif" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8336 Number of models: 1 Model: "" Number of chains: 6 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: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2305 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 1 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SY9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.62 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: 3.30 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 25 helices and 10 sheets defined 45.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 5 through 36 removed outlier: 3.675A pdb=" N ARG A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 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 99 through 104 removed outlier: 3.706A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 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 148 through 159 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.150A pdb=" N TYR A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.743A pdb=" N ALA A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 186 through 207 removed outlier: 4.229A pdb=" N SER A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.771A pdb=" N ASN A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.669A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.803A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.562A pdb=" N TYR N 33 " --> pdb=" O PHE N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 4 through 39 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 76 through 111 removed outlier: 3.760A pdb=" N VAL R 80 " --> pdb=" O ASN R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 124 removed outlier: 3.692A pdb=" N ARG R 124 " --> pdb=" O HIS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 154 removed outlier: 3.681A pdb=" N VAL R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Proline residue: R 136 - end of helix Processing helix chain 'R' and resid 174 through 213 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 218 through 254 Processing helix chain 'R' and resid 258 through 283 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 283 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79 removed outlier: 6.322A pdb=" N HIS A 37 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 87 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 39 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL A 89 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 41 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 38 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE A 110 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 40 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 112 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 42 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ASP A 114 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A 147 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 113 " --> pdb=" O ASN A 147 " (cutoff:3.500A) 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) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.595A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.242A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (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=AA4, 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=AA5, first strand: chain 'B' and resid 146 through 151 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=AA6, first strand: chain 'B' and resid 187 through 192 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=AA7, first strand: chain 'B' and resid 229 through 234 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=AA8, 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=AA9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.888A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1335 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: 2.74 Time building geometry restraints manager: 3.57 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: 120 2.66 - 3.22: 7959 3.22 - 3.78: 12954 3.78 - 4.34: 17208 4.34 - 4.90: 29084 Nonbonded interactions: 67325 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 67320 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: 0.680 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.960 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- 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 : 0.877 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: 0.2744 time to fit residues: 82.4127 Evaluate side-chains 225 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7259 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8518 Z= 0.254 Angle : 0.539 7.185 11549 Z= 0.294 Chirality : 0.043 0.187 1312 Planarity : 0.005 0.072 1456 Dihedral : 8.301 151.589 1193 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.09 % Allowed : 8.46 % Favored : 89.45 % 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: 1.88 (0.26), residues: 1037 helix: 2.76 (0.23), residues: 439 sheet: 0.89 (0.33), residues: 246 loop : -0.46 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 212 PHE 0.025 0.002 PHE A 87 TYR 0.025 0.002 TYR B 59 ARG 0.006 0.000 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 267 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8093 (p90) cc_final: 0.7791 (p90) REVERT: A 129 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8276 (ttpp) REVERT: A 134 ASN cc_start: 0.7616 (t0) cc_final: 0.7415 (t0) REVERT: A 226 ASN cc_start: 0.8065 (m110) cc_final: 0.7739 (m-40) REVERT: A 236 ASP cc_start: 0.7525 (t0) cc_final: 0.7041 (t0) REVERT: B 8 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7581 (ttt180) REVERT: B 13 GLN cc_start: 0.7988 (tp40) cc_final: 0.7095 (tp40) REVERT: B 45 MET cc_start: 0.8497 (mtp) cc_final: 0.8261 (mtp) REVERT: B 134 ARG cc_start: 0.7556 (ptp-110) cc_final: 0.7319 (ptp90) REVERT: B 317 CYS cc_start: 0.6636 (p) cc_final: 0.6432 (p) REVERT: N 14 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7114 (mm110) REVERT: N 32 ASN cc_start: 0.8591 (m-40) cc_final: 0.8376 (m110) REVERT: N 61 TYR cc_start: 0.8252 (m-80) cc_final: 0.7782 (m-80) REVERT: N 121 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7241 (mm-40) REVERT: R 149 MET cc_start: 0.5420 (tpt) cc_final: 0.5181 (tpt) REVERT: R 181 ILE cc_start: 0.7645 (mm) cc_final: 0.7404 (mm) REVERT: R 193 ILE cc_start: 0.7944 (tp) cc_final: 0.7687 (tp) REVERT: R 222 LYS cc_start: 0.7446 (tmtt) cc_final: 0.7133 (tmtt) REVERT: R 280 ILE cc_start: 0.8685 (mt) cc_final: 0.8460 (mm) REVERT: R 285 LYS cc_start: 0.8541 (pptt) cc_final: 0.8297 (pptt) outliers start: 19 outliers final: 18 residues processed: 250 average time/residue: 0.2572 time to fit residues: 81.9427 Evaluate side-chains 254 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 146 LEU Chi-restraints excluded: chain B residue 247 ASP 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 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 Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 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: 0.7261 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8518 Z= 0.231 Angle : 0.517 8.276 11549 Z= 0.278 Chirality : 0.041 0.190 1312 Planarity : 0.004 0.059 1456 Dihedral : 7.922 144.892 1193 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.42 % Allowed : 11.76 % Favored : 85.82 % 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: 1.92 (0.26), residues: 1037 helix: 2.79 (0.23), residues: 440 sheet: 1.00 (0.34), residues: 233 loop : -0.48 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 66 HIS 0.004 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.020 0.001 TYR B 59 ARG 0.003 0.000 ARG A 38 *********************** 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 274 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 252 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8149 (p90) cc_final: 0.7756 (p90) REVERT: A 134 ASN cc_start: 0.7776 (t0) cc_final: 0.7405 (t0) REVERT: A 226 ASN cc_start: 0.8041 (m110) cc_final: 0.7711 (m-40) REVERT: B 8 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7588 (ttt180) REVERT: B 13 GLN cc_start: 0.7984 (tp40) cc_final: 0.7094 (tp40) REVERT: B 134 ARG cc_start: 0.7479 (ptp-110) cc_final: 0.7222 (ptp90) REVERT: B 317 CYS cc_start: 0.6725 (p) cc_final: 0.6516 (p) REVERT: N 14 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7104 (mm-40) REVERT: N 32 ASN cc_start: 0.8589 (m-40) cc_final: 0.8366 (m110) REVERT: N 61 TYR cc_start: 0.8254 (m-80) cc_final: 0.7840 (m-80) REVERT: N 109 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: R 181 ILE cc_start: 0.7612 (mm) cc_final: 0.7364 (mm) REVERT: R 193 ILE cc_start: 0.7884 (tp) cc_final: 0.7630 (tp) REVERT: R 222 LYS cc_start: 0.7450 (tmtt) cc_final: 0.7119 (tmtt) REVERT: R 284 LYS cc_start: 0.7543 (ttmt) cc_final: 0.7177 (ttmt) outliers start: 22 outliers final: 18 residues processed: 257 average time/residue: 0.2527 time to fit residues: 83.2209 Evaluate side-chains 260 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 241 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 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 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 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: 0.5980 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 94 optimal weight: 0.0010 chunk 99 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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** B 119 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8518 Z= 0.152 Angle : 0.504 9.799 11549 Z= 0.262 Chirality : 0.039 0.132 1312 Planarity : 0.004 0.053 1456 Dihedral : 6.016 119.103 1193 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.08 % Allowed : 13.08 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1037 helix: 2.97 (0.23), residues: 440 sheet: 1.07 (0.34), residues: 230 loop : -0.41 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS A 212 PHE 0.017 0.001 PHE R 188 TYR 0.013 0.001 TYR R 241 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 279 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7357 (mtm-85) REVERT: A 76 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7583 (mmtp) REVERT: A 87 PHE cc_start: 0.8182 (p90) cc_final: 0.7764 (p90) REVERT: A 92 GLN cc_start: 0.8023 (mp10) cc_final: 0.7722 (mp10) REVERT: A 134 ASN cc_start: 0.7725 (t0) cc_final: 0.7312 (t0) REVERT: A 223 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: A 226 ASN cc_start: 0.7937 (m110) cc_final: 0.7628 (m-40) REVERT: B 8 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7556 (ttt180) REVERT: B 13 GLN cc_start: 0.7959 (tp40) cc_final: 0.7076 (tp40) REVERT: B 45 MET cc_start: 0.8482 (mtp) cc_final: 0.8215 (mtp) REVERT: B 212 ASP cc_start: 0.7534 (t0) cc_final: 0.7257 (t0) REVERT: B 317 CYS cc_start: 0.6828 (p) cc_final: 0.6548 (p) REVERT: N 32 ASN cc_start: 0.8466 (m-40) cc_final: 0.8225 (m110) REVERT: N 61 TYR cc_start: 0.8230 (m-80) cc_final: 0.7770 (m-80) REVERT: N 109 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.5645 (m-80) REVERT: R 193 ILE cc_start: 0.7854 (tp) cc_final: 0.7603 (tp) REVERT: R 222 LYS cc_start: 0.7337 (tmtt) cc_final: 0.6983 (tmtt) REVERT: R 284 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7146 (ttmt) outliers start: 28 outliers final: 14 residues processed: 262 average time/residue: 0.2589 time to fit residues: 87.1393 Evaluate side-chains 259 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 LYS 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 331 SER Chi-restraints excluded: chain N residue 109 PHE 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 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: 0.9980 chunk 56 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** N 32 ASN R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8518 Z= 0.196 Angle : 0.503 6.477 11549 Z= 0.267 Chirality : 0.040 0.213 1312 Planarity : 0.004 0.049 1456 Dihedral : 4.161 19.820 1193 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.53 % Allowed : 15.71 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.26), residues: 1037 helix: 2.90 (0.24), residues: 440 sheet: 1.00 (0.33), residues: 231 loop : -0.43 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 66 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.015 0.001 TYR B 59 ARG 0.003 0.000 ARG A 38 *********************** 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 269 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7081 (t0) cc_final: 0.6616 (t0) REVERT: A 76 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7599 (mmtp) REVERT: A 87 PHE cc_start: 0.8245 (p90) cc_final: 0.7809 (p90) REVERT: A 134 ASN cc_start: 0.7819 (t0) cc_final: 0.7568 (t0) REVERT: A 198 ASP cc_start: 0.6914 (t70) cc_final: 0.6558 (t0) REVERT: A 223 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6507 (m-30) REVERT: A 226 ASN cc_start: 0.7990 (m110) cc_final: 0.7664 (m-40) REVERT: A 236 ASP cc_start: 0.7547 (t0) cc_final: 0.7054 (t70) REVERT: B 8 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7541 (ttt180) REVERT: B 13 GLN cc_start: 0.7971 (tp40) cc_final: 0.7088 (tp40) REVERT: B 317 CYS cc_start: 0.6807 (p) cc_final: 0.6502 (p) REVERT: N 32 ASN cc_start: 0.8489 (m110) cc_final: 0.8202 (m110) REVERT: N 61 TYR cc_start: 0.8241 (m-80) cc_final: 0.7761 (m-80) REVERT: N 109 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6085 (m-80) REVERT: R 193 ILE cc_start: 0.7910 (tp) cc_final: 0.7665 (tp) REVERT: R 222 LYS cc_start: 0.7405 (tmtt) cc_final: 0.7044 (tmtt) REVERT: R 284 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7202 (ttmt) outliers start: 23 outliers final: 13 residues processed: 254 average time/residue: 0.2561 time to fit residues: 83.1946 Evaluate side-chains 259 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 N residue 109 PHE 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 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: 2.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** B 119 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1992 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= 0.187 Angle : 0.512 9.683 11549 Z= 0.268 Chirality : 0.040 0.154 1312 Planarity : 0.004 0.045 1456 Dihedral : 4.044 19.598 1193 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.97 % Allowed : 16.59 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1037 helix: 2.89 (0.24), residues: 440 sheet: 0.95 (0.33), residues: 231 loop : -0.41 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 66 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.013 0.001 TYR B 59 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 271 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7088 (t0) cc_final: 0.6609 (t0) REVERT: A 76 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7572 (mmtp) REVERT: A 87 PHE cc_start: 0.8234 (p90) cc_final: 0.7724 (p90) REVERT: A 134 ASN cc_start: 0.7842 (t0) cc_final: 0.7557 (t0) REVERT: A 169 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6478 (mm-30) REVERT: A 198 ASP cc_start: 0.6926 (t70) cc_final: 0.6546 (t0) REVERT: A 223 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: A 226 ASN cc_start: 0.7995 (m110) cc_final: 0.7635 (m-40) REVERT: A 236 ASP cc_start: 0.7538 (t0) cc_final: 0.7233 (t70) REVERT: B 8 ARG cc_start: 0.7804 (ttt180) cc_final: 0.7538 (ttt180) REVERT: B 13 GLN cc_start: 0.7967 (tp40) cc_final: 0.7087 (tp40) REVERT: B 317 CYS cc_start: 0.6822 (p) cc_final: 0.6525 (p) REVERT: N 32 ASN cc_start: 0.8429 (m110) cc_final: 0.8192 (m110) REVERT: N 61 TYR cc_start: 0.8134 (m-80) cc_final: 0.7638 (m-80) REVERT: N 109 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: R 193 ILE cc_start: 0.7900 (tp) cc_final: 0.7659 (tp) REVERT: R 222 LYS cc_start: 0.7399 (tmtt) cc_final: 0.7033 (tmtt) REVERT: R 284 LYS cc_start: 0.7571 (ttmt) cc_final: 0.7197 (ttmt) outliers start: 27 outliers final: 19 residues processed: 252 average time/residue: 0.2679 time to fit residues: 86.2603 Evaluate side-chains 262 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 240 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 327 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** B 119 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8518 Z= 0.184 Angle : 0.505 7.173 11549 Z= 0.265 Chirality : 0.040 0.177 1312 Planarity : 0.004 0.043 1456 Dihedral : 4.004 19.692 1193 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.97 % Allowed : 16.81 % Favored : 80.22 % 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: 1.99 (0.26), residues: 1037 helix: 2.89 (0.23), residues: 440 sheet: 0.90 (0.33), residues: 231 loop : -0.37 (0.33), residues: 366 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 0.016 0.001 PHE R 188 TYR 0.012 0.001 TYR B 59 ARG 0.003 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 280 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7089 (t0) cc_final: 0.6605 (t0) REVERT: A 55 GLN cc_start: 0.7306 (pt0) cc_final: 0.6964 (pt0) REVERT: A 76 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7569 (mmtp) REVERT: A 87 PHE cc_start: 0.8256 (p90) cc_final: 0.7726 (p90) REVERT: A 122 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7984 (tp40) REVERT: A 134 ASN cc_start: 0.7865 (t0) cc_final: 0.7558 (t0) REVERT: A 169 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6460 (mm-30) REVERT: A 198 ASP cc_start: 0.6935 (t70) cc_final: 0.6543 (t0) REVERT: A 223 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: A 226 ASN cc_start: 0.7990 (m110) cc_final: 0.7590 (m-40) REVERT: B 8 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7534 (ttt180) REVERT: B 13 GLN cc_start: 0.7966 (tp40) cc_final: 0.7087 (tp40) REVERT: B 204 CYS cc_start: 0.7045 (m) cc_final: 0.6792 (m) REVERT: B 317 CYS cc_start: 0.6837 (p) cc_final: 0.6598 (p) REVERT: N 32 ASN cc_start: 0.8415 (m110) cc_final: 0.8171 (m110) REVERT: N 61 TYR cc_start: 0.8131 (m-80) cc_final: 0.7624 (m-80) REVERT: N 109 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: R 193 ILE cc_start: 0.7895 (tp) cc_final: 0.7658 (tp) REVERT: R 222 LYS cc_start: 0.7405 (tmtt) cc_final: 0.7036 (tmtt) REVERT: R 284 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7275 (ttmt) outliers start: 27 outliers final: 20 residues processed: 260 average time/residue: 0.2497 time to fit residues: 83.2127 Evaluate side-chains 276 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 327 VAL Chi-restraints excluded: chain N residue 36 ASN 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 49 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: 2.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 19 ASN B 119 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2198 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= 0.203 Angle : 0.513 6.668 11549 Z= 0.270 Chirality : 0.040 0.173 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.028 19.811 1193 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.97 % Allowed : 18.02 % Favored : 79.01 % 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: 1.95 (0.26), residues: 1037 helix: 2.86 (0.23), residues: 441 sheet: 0.80 (0.33), residues: 233 loop : -0.35 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 300 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG A 38 *********************** 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 285 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7096 (t0) cc_final: 0.6621 (t0) REVERT: A 55 GLN cc_start: 0.7316 (pt0) cc_final: 0.6976 (pt0) REVERT: A 76 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7561 (mmtp) REVERT: A 87 PHE cc_start: 0.8277 (p90) cc_final: 0.7714 (p90) REVERT: A 122 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7922 (tp-100) REVERT: A 134 ASN cc_start: 0.7906 (t0) cc_final: 0.7592 (t0) REVERT: A 135 ARG cc_start: 0.6807 (mmp80) cc_final: 0.6494 (mtp85) REVERT: A 169 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6454 (mm-30) REVERT: A 198 ASP cc_start: 0.6944 (t70) cc_final: 0.6557 (t0) REVERT: A 223 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: A 226 ASN cc_start: 0.8014 (m110) cc_final: 0.7617 (m-40) REVERT: B 8 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7518 (ttt180) REVERT: B 13 GLN cc_start: 0.7969 (tp40) cc_final: 0.7094 (tp40) REVERT: B 204 CYS cc_start: 0.7121 (m) cc_final: 0.6852 (m) REVERT: B 317 CYS cc_start: 0.6843 (p) cc_final: 0.6601 (p) REVERT: N 32 ASN cc_start: 0.8404 (m110) cc_final: 0.8157 (m110) REVERT: N 61 TYR cc_start: 0.8239 (m-80) cc_final: 0.7719 (m-80) REVERT: N 109 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: R 193 ILE cc_start: 0.7898 (tp) cc_final: 0.7666 (tp) REVERT: R 222 LYS cc_start: 0.7411 (tmtt) cc_final: 0.7053 (tmtt) REVERT: R 284 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7247 (ttmt) outliers start: 27 outliers final: 22 residues processed: 264 average time/residue: 0.2534 time to fit residues: 85.5797 Evaluate side-chains 281 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 175 THR 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 327 VAL Chi-restraints excluded: chain N residue 36 ASN 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 49 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 119 ASN B 155 ASN R 31 ASN ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8518 Z= 0.191 Angle : 0.522 8.683 11549 Z= 0.273 Chirality : 0.040 0.159 1312 Planarity : 0.004 0.041 1456 Dihedral : 3.990 19.678 1193 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.08 % Allowed : 18.35 % Favored : 78.57 % 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: 1.95 (0.26), residues: 1037 helix: 2.85 (0.23), residues: 443 sheet: 0.77 (0.33), residues: 233 loop : -0.34 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 300 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.017 0.001 TYR R 106 ARG 0.004 0.000 ARG A 38 *********************** 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 278 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7089 (t0) cc_final: 0.6610 (t0) REVERT: A 55 GLN cc_start: 0.7313 (pt0) cc_final: 0.6977 (pt0) REVERT: A 76 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7559 (mmtp) REVERT: A 79 VAL cc_start: 0.8670 (t) cc_final: 0.8459 (m) REVERT: A 87 PHE cc_start: 0.8268 (p90) cc_final: 0.7712 (p90) REVERT: A 122 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7968 (tp40) REVERT: A 134 ASN cc_start: 0.7929 (t0) cc_final: 0.7604 (t0) REVERT: A 135 ARG cc_start: 0.6877 (mmp80) cc_final: 0.6547 (mmp80) REVERT: A 169 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6621 (mm-30) REVERT: A 198 ASP cc_start: 0.6939 (t70) cc_final: 0.6558 (t0) REVERT: A 223 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: A 226 ASN cc_start: 0.7994 (m110) cc_final: 0.7602 (m-40) REVERT: A 236 ASP cc_start: 0.7561 (t0) cc_final: 0.7311 (t70) REVERT: B 8 ARG cc_start: 0.7811 (ttt180) cc_final: 0.7513 (ttt180) REVERT: B 13 GLN cc_start: 0.7963 (tp40) cc_final: 0.7085 (tp40) REVERT: B 317 CYS cc_start: 0.6857 (p) cc_final: 0.6598 (p) REVERT: G 41 CYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6534 (p) REVERT: N 32 ASN cc_start: 0.8384 (m110) cc_final: 0.8157 (m110) REVERT: N 61 TYR cc_start: 0.8138 (m-80) cc_final: 0.7629 (m-80) REVERT: N 109 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: R 106 TYR cc_start: 0.7952 (m-10) cc_final: 0.7674 (m-10) REVERT: R 193 ILE cc_start: 0.7796 (tp) cc_final: 0.7577 (tp) REVERT: R 222 LYS cc_start: 0.7435 (tmtt) cc_final: 0.7044 (tmtt) REVERT: R 284 LYS cc_start: 0.7564 (ttmt) cc_final: 0.7205 (ttmt) outliers start: 28 outliers final: 23 residues processed: 256 average time/residue: 0.2588 time to fit residues: 84.7463 Evaluate side-chains 278 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR 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 175 THR 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 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 36 ASN 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 49 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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** ** R 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8518 Z= 0.253 Angle : 0.545 8.404 11549 Z= 0.287 Chirality : 0.041 0.162 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.125 20.656 1193 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.41 % Allowed : 18.02 % Favored : 78.57 % 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: 1.82 (0.26), residues: 1037 helix: 2.74 (0.23), residues: 442 sheet: 0.70 (0.32), residues: 233 loop : -0.40 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 300 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.001 PHE R 188 TYR 0.019 0.002 TYR B 59 ARG 0.004 0.000 ARG A 38 ********************** 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 286 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 255 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7124 (t0) cc_final: 0.6696 (t0) REVERT: A 55 GLN cc_start: 0.7346 (pt0) cc_final: 0.7035 (pt0) REVERT: A 76 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7558 (mmtp) REVERT: A 87 PHE cc_start: 0.8289 (p90) cc_final: 0.7711 (p90) REVERT: A 122 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7921 (tp40) REVERT: A 198 ASP cc_start: 0.6966 (t70) cc_final: 0.6593 (t0) REVERT: A 223 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: A 226 ASN cc_start: 0.8062 (m110) cc_final: 0.7692 (m-40) REVERT: B 8 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7527 (ttt180) REVERT: B 13 GLN cc_start: 0.7977 (tp40) cc_final: 0.7106 (tp40) REVERT: B 317 CYS cc_start: 0.6850 (p) cc_final: 0.6603 (p) REVERT: G 41 CYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6660 (p) REVERT: N 32 ASN cc_start: 0.8447 (m110) cc_final: 0.8184 (m110) REVERT: N 61 TYR cc_start: 0.8149 (m-80) cc_final: 0.7646 (m-80) REVERT: N 109 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: R 193 ILE cc_start: 0.7908 (tp) cc_final: 0.7680 (tp) REVERT: R 222 LYS cc_start: 0.7480 (tmtt) cc_final: 0.7091 (tmtt) REVERT: R 284 LYS cc_start: 0.7621 (ttmt) cc_final: 0.7260 (ttmt) outliers start: 31 outliers final: 26 residues processed: 264 average time/residue: 0.2612 time to fit residues: 89.0074 Evaluate side-chains 284 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 254 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 36 THR 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 175 THR 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 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 36 ASN 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 130 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 149 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 119 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3873 r_free = 0.3873 target = 0.138886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120959 restraints weight = 12434.908| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.17 r_work: 0.3512 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8518 Z= 0.249 Angle : 0.552 8.971 11549 Z= 0.288 Chirality : 0.042 0.185 1312 Planarity : 0.004 0.042 1456 Dihedral : 4.148 20.772 1193 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.19 % Allowed : 19.12 % Favored : 77.69 % 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: 2.69 (0.23), residues: 441 sheet: 0.63 (0.33), residues: 233 loop : -0.44 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 300 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE R 188 TYR 0.026 0.002 TYR R 106 ARG 0.004 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.42 seconds wall clock time: 44 minutes 53.28 seconds (2693.28 seconds total)