Starting phenix.real_space_refine on Sun Apr 5 08:06:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ly3_63502/04_2026/9ly3_63502_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ly3_63502/04_2026/9ly3_63502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ly3_63502/04_2026/9ly3_63502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ly3_63502/04_2026/9ly3_63502.map" model { file = "/net/cci-nas-00/data/ceres_data/9ly3_63502/04_2026/9ly3_63502_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ly3_63502/04_2026/9ly3_63502_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.033 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 43 5.16 5 C 5628 2.51 5 N 1470 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8771 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 274 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2659 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 22, 'TRANS': 311} Chain breaks: 2 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1551 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1587 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Chain: "R" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2700 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 326} Chain breaks: 6 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8771 At special positions: 0 Unit cell: (83.95, 100.74, 201.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 5 15.00 O 1625 8.00 N 1470 7.00 C 5628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 289.8 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 16 sheets defined 30.8% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.873A pdb=" N PHE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.813A pdb=" N ARG B 282 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.659A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.609A pdb=" N HIS E 190 " --> pdb=" O ASP E 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 56 Processing helix chain 'R' and resid 173 through 175 No H-bonds generated for 'chain 'R' and resid 173 through 175' Processing helix chain 'R' and resid 176 through 212 removed outlier: 4.074A pdb=" N GLU R 182 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY R 194 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 277 through 311 removed outlier: 3.970A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 347 removed outlier: 4.093A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 358 through 388 removed outlier: 3.923A pdb=" N ILE R 362 " --> pdb=" O ASN R 358 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE R 363 " --> pdb=" O LYS R 359 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 4.265A pdb=" N LYS R 388 " --> pdb=" O VAL R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 407 Processing helix chain 'R' and resid 407 through 418 removed outlier: 4.291A pdb=" N LEU R 411 " --> pdb=" O LEU R 407 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 425 removed outlier: 3.620A pdb=" N PHE R 424 " --> pdb=" O TYR R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.225A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 473 Processing sheet with id=AA1, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.783A pdb=" N VAL B 8 " --> pdb=" O SEP R 523 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SEP R 523 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS B 10 " --> pdb=" O ALA R 521 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 4.010A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 57 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 186 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.944A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.602A pdb=" N VAL C 8 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 15 removed outlier: 8.469A pdb=" N SER C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER C 55 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.950A pdb=" N TYR C 112 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 130 through 134 removed outlier: 4.732A pdb=" N ALA C 147 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 194 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY C 149 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C 192 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU C 151 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER C 190 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS C 153 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU C 188 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 130 through 134 removed outlier: 4.732A pdb=" N ALA C 147 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 194 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY C 149 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C 192 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU C 151 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER C 190 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS C 153 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU C 188 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.024A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.594A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.862A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 117 through 119 removed outlier: 4.064A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 147 through 151 440 hydrogen bonds defined for protein. 1176 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: 1.40 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2745 1.34 - 1.46: 2140 1.46 - 1.58: 4012 1.58 - 1.69: 18 1.69 - 1.81: 57 Bond restraints: 8972 Sorted by residual: bond pdb=" OG1 TPO R 519 " pdb=" P TPO R 519 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" OG1 TPO R 520 " pdb=" P TPO R 520 " ideal model delta sigma weight residual 1.717 1.615 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3P TPO R 519 " pdb=" P TPO R 519 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O2P TPO R 519 " pdb=" P TPO R 519 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O2P TPO R 520 " pdb=" P TPO R 520 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11971 1.63 - 3.25: 165 3.25 - 4.88: 33 4.88 - 6.50: 7 6.50 - 8.13: 6 Bond angle restraints: 12182 Sorted by residual: angle pdb=" C ASN E 138 " pdb=" CA ASN E 138 " pdb=" CB ASN E 138 " ideal model delta sigma weight residual 116.34 111.28 5.06 1.40e+00 5.10e-01 1.31e+01 angle pdb=" CA VAL C 194 " pdb=" C VAL C 194 " pdb=" N PRO C 195 " ideal model delta sigma weight residual 116.57 119.27 -2.70 9.80e-01 1.04e+00 7.57e+00 angle pdb=" OG1 TPO R 519 " pdb=" P TPO R 519 " pdb=" O1P TPO R 519 " ideal model delta sigma weight residual 100.43 108.56 -8.13 3.00e+00 1.11e-01 7.35e+00 angle pdb=" OG1 TPO R 520 " pdb=" P TPO R 520 " pdb=" O1P TPO R 520 " ideal model delta sigma weight residual 100.43 108.46 -8.03 3.00e+00 1.11e-01 7.16e+00 angle pdb=" CA ARG A 20 " pdb=" CB ARG A 20 " pdb=" CG ARG A 20 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.70e+00 ... (remaining 12177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 5089 15.98 - 31.97: 177 31.97 - 47.95: 46 47.95 - 63.93: 6 63.93 - 79.91: 4 Dihedral angle restraints: 5322 sinusoidal: 2062 harmonic: 3260 Sorted by residual: dihedral pdb=" CA ASN B 15 " pdb=" C ASN B 15 " pdb=" N GLY B 16 " pdb=" CA GLY B 16 " ideal model delta harmonic sigma weight residual -180.00 -155.18 -24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA CYS B 14 " pdb=" C CYS B 14 " pdb=" N ASN B 15 " pdb=" CA ASN B 15 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ARG C 41 " pdb=" C ARG C 41 " pdb=" N GLN C 42 " pdb=" CA GLN C 42 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 865 0.027 - 0.055: 340 0.055 - 0.082: 86 0.082 - 0.110: 58 0.110 - 0.137: 38 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA ILE B 231 " pdb=" N ILE B 231 " pdb=" C ILE B 231 " pdb=" CB ILE B 231 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE E 3 " pdb=" N ILE E 3 " pdb=" C ILE E 3 " pdb=" CB ILE E 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA VAL R 31 " pdb=" N VAL R 31 " pdb=" C VAL R 31 " pdb=" CB VAL R 31 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1384 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 299 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE R 299 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE R 299 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU R 300 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 288 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.68e+00 pdb=" C PHE R 288 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE R 288 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU R 289 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 119 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO E 120 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 120 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 120 " -0.016 5.00e-02 4.00e+02 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 92 2.60 - 3.17: 7871 3.17 - 3.75: 13159 3.75 - 4.32: 18367 4.32 - 4.90: 30650 Nonbonded interactions: 70139 Sorted by model distance: nonbonded pdb=" OD1 ASP A 17 " pdb=" NH2 ARG A 20 " model vdw 2.023 3.120 nonbonded pdb=" OG SER E 29 " pdb=" O1P SEP R 522 " model vdw 2.089 3.040 nonbonded pdb=" OE1 GLN C 181 " pdb=" OG SER C 187 " model vdw 2.116 3.040 nonbonded pdb=" N TPO R 519 " pdb=" O2P TPO R 519 " model vdw 2.138 3.120 nonbonded pdb=" O LEU R 215 " pdb=" ND2 ASN R 220 " model vdw 2.163 3.120 ... (remaining 70134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.780 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 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 0.104 8972 Z= 0.178 Angle : 0.552 8.131 12182 Z= 0.306 Chirality : 0.039 0.137 1387 Planarity : 0.003 0.028 1517 Dihedral : 9.481 79.913 3218 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1076 helix: 1.27 (0.31), residues: 283 sheet: 0.77 (0.30), residues: 327 loop : 0.12 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.015 0.001 TYR R 191 PHE 0.006 0.001 PHE B 117 TRP 0.006 0.001 TRP R 298 HIS 0.002 0.000 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8972) covalent geometry : angle 0.55245 (12182) hydrogen bonds : bond 0.14608 ( 422) hydrogen bonds : angle 6.69751 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 PHE cc_start: 0.6972 (m-80) cc_final: 0.6490 (m-80) REVERT: B 208 TYR cc_start: 0.8513 (m-80) cc_final: 0.8264 (m-80) REVERT: B 220 VAL cc_start: 0.7950 (t) cc_final: 0.7741 (m) REVERT: B 248 GLN cc_start: 0.8131 (tt0) cc_final: 0.7724 (tt0) REVERT: B 249 TYR cc_start: 0.7617 (m-80) cc_final: 0.7261 (m-80) REVERT: C 76 ASP cc_start: 0.7789 (t0) cc_final: 0.7564 (t0) REVERT: C 153 LYS cc_start: 0.8089 (tttp) cc_final: 0.7750 (ttpt) REVERT: C 186 TYR cc_start: 0.7953 (m-80) cc_final: 0.7696 (m-80) REVERT: E 10 SER cc_start: 0.8026 (m) cc_final: 0.7813 (p) REVERT: R 224 MET cc_start: 0.6705 (ttp) cc_final: 0.6411 (ppp) REVERT: R 329 TRP cc_start: 0.5751 (m100) cc_final: 0.5476 (m100) REVERT: R 352 TRP cc_start: 0.4642 (OUTLIER) cc_final: 0.4014 (m100) REVERT: R 413 LEU cc_start: 0.8954 (mt) cc_final: 0.8700 (mm) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.1210 time to fit residues: 35.0669 Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 352 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS B 299 ASN E 138 ASN R 45 GLN R 225 HIS ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 442 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.145058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.103773 restraints weight = 21888.192| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.79 r_work: 0.3488 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8972 Z= 0.208 Angle : 0.729 10.541 12182 Z= 0.364 Chirality : 0.046 0.213 1387 Planarity : 0.005 0.042 1517 Dihedral : 4.946 59.569 1218 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 1.66 % Allowed : 9.47 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1076 helix: 1.35 (0.29), residues: 291 sheet: 0.64 (0.29), residues: 318 loop : -0.11 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 65 TYR 0.018 0.002 TYR E 92 PHE 0.038 0.002 PHE R 287 TRP 0.011 0.002 TRP C 106 HIS 0.012 0.002 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8972) covalent geometry : angle 0.72859 (12182) hydrogen bonds : bond 0.04248 ( 422) hydrogen bonds : angle 5.07768 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 PHE cc_start: 0.7691 (m-80) cc_final: 0.6813 (m-80) REVERT: B 104 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7675 (tt) REVERT: B 220 VAL cc_start: 0.7798 (t) cc_final: 0.7440 (m) REVERT: E 18 ASP cc_start: 0.7689 (t0) cc_final: 0.7441 (t0) REVERT: E 186 ASP cc_start: 0.9113 (m-30) cc_final: 0.8787 (p0) REVERT: E 211 ASN cc_start: 0.6881 (t0) cc_final: 0.6411 (t0) REVERT: R 440 GLN cc_start: 0.8308 (pp30) cc_final: 0.8042 (pp30) outliers start: 16 outliers final: 13 residues processed: 145 average time/residue: 0.0923 time to fit residues: 18.7354 Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 429 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 GLN E 138 ASN ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 451 GLN ** 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 = 0.4437 r_free = 0.4437 target = 0.144409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104232 restraints weight = 21693.044| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.71 r_work: 0.3486 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8972 Z= 0.154 Angle : 0.651 12.236 12182 Z= 0.323 Chirality : 0.043 0.208 1387 Planarity : 0.004 0.041 1517 Dihedral : 4.613 32.298 1216 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 2.71 % Allowed : 10.82 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1076 helix: 1.44 (0.30), residues: 288 sheet: 0.68 (0.29), residues: 321 loop : -0.20 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.016 0.002 TYR R 421 PHE 0.015 0.002 PHE R 287 TRP 0.010 0.001 TRP R 298 HIS 0.009 0.002 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8972) covalent geometry : angle 0.65114 (12182) hydrogen bonds : bond 0.03941 ( 422) hydrogen bonds : angle 4.95428 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 PHE cc_start: 0.7740 (m-80) cc_final: 0.6845 (m-80) REVERT: B 104 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7694 (tt) REVERT: B 220 VAL cc_start: 0.7748 (t) cc_final: 0.7271 (m) REVERT: C 92 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: E 186 ASP cc_start: 0.9140 (m-30) cc_final: 0.8737 (p0) REVERT: E 211 ASN cc_start: 0.6821 (t0) cc_final: 0.6384 (t0) REVERT: R 237 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7501 (tp) REVERT: R 241 ASP cc_start: 0.8680 (t70) cc_final: 0.7777 (m-30) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 0.0832 time to fit residues: 15.6071 Evaluate side-chains 119 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 429 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.142566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.100298 restraints weight = 21762.427| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.73 r_work: 0.3437 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8972 Z= 0.223 Angle : 0.692 13.004 12182 Z= 0.346 Chirality : 0.044 0.205 1387 Planarity : 0.004 0.042 1517 Dihedral : 4.865 35.329 1216 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 3.23 % Allowed : 11.76 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1076 helix: 1.17 (0.30), residues: 295 sheet: 0.53 (0.29), residues: 321 loop : -0.43 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 181 TYR 0.020 0.002 TYR E 92 PHE 0.022 0.002 PHE B 268 TRP 0.036 0.002 TRP A 14 HIS 0.010 0.002 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 8972) covalent geometry : angle 0.69179 (12182) hydrogen bonds : bond 0.03953 ( 422) hydrogen bonds : angle 5.09431 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7373 (t60) cc_final: 0.7079 (t60) REVERT: B 104 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7832 (tt) REVERT: B 220 VAL cc_start: 0.7940 (t) cc_final: 0.7474 (m) REVERT: E 186 ASP cc_start: 0.9156 (m-30) cc_final: 0.8742 (p0) REVERT: R 440 GLN cc_start: 0.8512 (pp30) cc_final: 0.8293 (pp30) REVERT: R 441 MET cc_start: 0.8164 (mmm) cc_final: 0.7833 (mmm) outliers start: 31 outliers final: 19 residues processed: 139 average time/residue: 0.0804 time to fit residues: 16.2521 Evaluate side-chains 121 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 453 PHE Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 442 HIS ** R 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.142719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099702 restraints weight = 21687.028| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.33 r_work: 0.3492 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8972 Z= 0.137 Angle : 0.644 13.057 12182 Z= 0.320 Chirality : 0.043 0.201 1387 Planarity : 0.004 0.041 1517 Dihedral : 4.753 30.395 1216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.56 % Rotamer: Outliers : 3.23 % Allowed : 13.01 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1076 helix: 1.13 (0.29), residues: 295 sheet: 0.69 (0.29), residues: 323 loop : -0.43 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 282 TYR 0.013 0.001 TYR E 92 PHE 0.019 0.001 PHE B 268 TRP 0.027 0.001 TRP A 14 HIS 0.018 0.002 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8972) covalent geometry : angle 0.64424 (12182) hydrogen bonds : bond 0.03711 ( 422) hydrogen bonds : angle 4.87822 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7280 (t60) cc_final: 0.7016 (t60) REVERT: B 62 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7399 (ttm-80) REVERT: B 104 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 220 VAL cc_start: 0.7895 (t) cc_final: 0.7657 (m) REVERT: B 248 GLN cc_start: 0.7808 (tt0) cc_final: 0.7405 (tt0) REVERT: C 185 LEU cc_start: 0.7745 (tp) cc_final: 0.7524 (tp) REVERT: E 18 ASP cc_start: 0.7344 (t0) cc_final: 0.7052 (t0) REVERT: E 186 ASP cc_start: 0.9109 (m-30) cc_final: 0.8731 (p0) REVERT: R 224 MET cc_start: 0.6563 (ptm) cc_final: 0.5871 (mmp) REVERT: R 302 GLU cc_start: 0.7235 (mt-10) cc_final: 0.7030 (mt-10) REVERT: R 329 TRP cc_start: 0.5784 (m100) cc_final: 0.5554 (m100) REVERT: R 440 GLN cc_start: 0.8520 (pp30) cc_final: 0.8108 (pp30) REVERT: R 441 MET cc_start: 0.8125 (mmm) cc_final: 0.7706 (mmm) outliers start: 31 outliers final: 20 residues processed: 135 average time/residue: 0.0805 time to fit residues: 15.8664 Evaluate side-chains 128 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 453 PHE Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.140828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.097822 restraints weight = 21528.986| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.67 r_work: 0.3442 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8972 Z= 0.221 Angle : 0.697 13.890 12182 Z= 0.350 Chirality : 0.045 0.218 1387 Planarity : 0.004 0.042 1517 Dihedral : 4.988 34.839 1216 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 3.43 % Allowed : 13.11 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1076 helix: 1.21 (0.29), residues: 289 sheet: 0.60 (0.28), residues: 330 loop : -0.47 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 219 TYR 0.020 0.002 TYR E 92 PHE 0.030 0.002 PHE R 375 TRP 0.021 0.002 TRP A 14 HIS 0.008 0.002 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 8972) covalent geometry : angle 0.69701 (12182) hydrogen bonds : bond 0.03883 ( 422) hydrogen bonds : angle 5.07698 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7222 (t60) cc_final: 0.6944 (t60) REVERT: B 62 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7420 (ttm-80) REVERT: B 75 PHE cc_start: 0.7739 (m-80) cc_final: 0.6889 (m-80) REVERT: B 220 VAL cc_start: 0.8062 (t) cc_final: 0.7759 (m) REVERT: C 185 LEU cc_start: 0.8116 (tp) cc_final: 0.7826 (tp) REVERT: E 143 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7745 (ttt180) REVERT: E 186 ASP cc_start: 0.9134 (m-30) cc_final: 0.8733 (p0) REVERT: R 224 MET cc_start: 0.6540 (ptm) cc_final: 0.5807 (mmp) REVERT: R 302 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7071 (mt-10) REVERT: R 440 GLN cc_start: 0.8634 (pp30) cc_final: 0.8321 (pp30) outliers start: 33 outliers final: 22 residues processed: 140 average time/residue: 0.0892 time to fit residues: 17.7119 Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 453 PHE Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.0050 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.141681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099701 restraints weight = 21437.078| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.47 r_work: 0.3465 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8972 Z= 0.143 Angle : 0.650 12.742 12182 Z= 0.326 Chirality : 0.043 0.203 1387 Planarity : 0.004 0.043 1517 Dihedral : 4.834 36.132 1216 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 2.19 % Allowed : 15.61 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1076 helix: 1.02 (0.29), residues: 295 sheet: 0.65 (0.29), residues: 330 loop : -0.54 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 282 TYR 0.020 0.001 TYR R 136 PHE 0.022 0.001 PHE R 375 TRP 0.018 0.001 TRP A 14 HIS 0.023 0.002 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8972) covalent geometry : angle 0.64985 (12182) hydrogen bonds : bond 0.03764 ( 422) hydrogen bonds : angle 4.93066 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7183 (t60) cc_final: 0.6923 (t60) REVERT: B 62 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7346 (ttm-80) REVERT: B 75 PHE cc_start: 0.7654 (m-80) cc_final: 0.6831 (m-80) REVERT: B 192 MET cc_start: 0.7765 (ttt) cc_final: 0.7482 (mtm) REVERT: B 220 VAL cc_start: 0.7922 (t) cc_final: 0.7700 (m) REVERT: C 185 LEU cc_start: 0.8148 (tp) cc_final: 0.7860 (tp) REVERT: E 143 ARG cc_start: 0.7943 (ttt180) cc_final: 0.7667 (ttm170) REVERT: E 174 TYR cc_start: 0.7679 (m-80) cc_final: 0.7108 (m-10) REVERT: E 186 ASP cc_start: 0.9115 (m-30) cc_final: 0.8762 (p0) REVERT: R 224 MET cc_start: 0.6476 (ptm) cc_final: 0.5784 (mmp) REVERT: R 302 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6669 (mm-30) outliers start: 21 outliers final: 19 residues processed: 122 average time/residue: 0.0889 time to fit residues: 15.5253 Evaluate side-chains 117 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.0970 chunk 54 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.141364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098976 restraints weight = 21346.009| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.44 r_work: 0.3459 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8972 Z= 0.175 Angle : 0.674 14.996 12182 Z= 0.336 Chirality : 0.043 0.237 1387 Planarity : 0.004 0.043 1517 Dihedral : 4.852 38.980 1216 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.81 % Allowed : 15.19 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1076 helix: 1.06 (0.29), residues: 289 sheet: 0.60 (0.29), residues: 330 loop : -0.54 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 282 TYR 0.017 0.002 TYR R 136 PHE 0.023 0.002 PHE R 375 TRP 0.016 0.002 TRP A 14 HIS 0.018 0.002 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8972) covalent geometry : angle 0.67395 (12182) hydrogen bonds : bond 0.03835 ( 422) hydrogen bonds : angle 4.99071 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7165 (t60) cc_final: 0.6892 (t60) REVERT: B 75 PHE cc_start: 0.7666 (m-80) cc_final: 0.6858 (m-80) REVERT: B 220 VAL cc_start: 0.8003 (t) cc_final: 0.7769 (m) REVERT: B 248 GLN cc_start: 0.7838 (tt0) cc_final: 0.7497 (tt0) REVERT: C 185 LEU cc_start: 0.8179 (tp) cc_final: 0.7862 (tp) REVERT: E 143 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7667 (ttm170) REVERT: E 174 TYR cc_start: 0.7689 (m-80) cc_final: 0.7267 (m-10) REVERT: E 186 ASP cc_start: 0.9102 (m-30) cc_final: 0.8766 (p0) REVERT: R 224 MET cc_start: 0.6422 (ptm) cc_final: 0.5722 (mmm) REVERT: R 231 MET cc_start: 0.8216 (mmm) cc_final: 0.7871 (mmm) REVERT: R 302 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6754 (mm-30) outliers start: 27 outliers final: 24 residues processed: 128 average time/residue: 0.0866 time to fit residues: 15.8432 Evaluate side-chains 127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 451 GLN Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.142545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101840 restraints weight = 21331.972| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.49 r_work: 0.3477 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8972 Z= 0.135 Angle : 0.676 13.725 12182 Z= 0.328 Chirality : 0.043 0.227 1387 Planarity : 0.004 0.044 1517 Dihedral : 4.777 41.165 1216 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 2.19 % Allowed : 16.23 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1076 helix: 0.93 (0.29), residues: 295 sheet: 0.66 (0.29), residues: 332 loop : -0.63 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 282 TYR 0.031 0.001 TYR E 141 PHE 0.021 0.001 PHE R 375 TRP 0.016 0.001 TRP A 14 HIS 0.024 0.002 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8972) covalent geometry : angle 0.67573 (12182) hydrogen bonds : bond 0.03645 ( 422) hydrogen bonds : angle 4.88630 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7022 (t60) cc_final: 0.6758 (t60) REVERT: B 75 PHE cc_start: 0.7681 (m-80) cc_final: 0.6955 (m-80) REVERT: B 192 MET cc_start: 0.7478 (ttt) cc_final: 0.7194 (mtm) REVERT: B 220 VAL cc_start: 0.7942 (t) cc_final: 0.7726 (m) REVERT: C 185 LEU cc_start: 0.8180 (tp) cc_final: 0.7889 (tp) REVERT: E 174 TYR cc_start: 0.7696 (m-80) cc_final: 0.7281 (m-10) REVERT: E 186 ASP cc_start: 0.9094 (m-30) cc_final: 0.8759 (p0) REVERT: R 224 MET cc_start: 0.6327 (ptm) cc_final: 0.6125 (ptm) REVERT: R 302 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6716 (mt-10) outliers start: 21 outliers final: 21 residues processed: 123 average time/residue: 0.0854 time to fit residues: 15.0008 Evaluate side-chains 120 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 451 GLN Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 102 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN R 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.148822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107316 restraints weight = 21425.055| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.64 r_work: 0.3455 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8972 Z= 0.141 Angle : 0.664 11.454 12182 Z= 0.332 Chirality : 0.043 0.233 1387 Planarity : 0.004 0.044 1517 Dihedral : 4.768 42.161 1216 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 2.39 % Allowed : 16.44 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1076 helix: 1.00 (0.29), residues: 295 sheet: 0.70 (0.29), residues: 332 loop : -0.64 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 282 TYR 0.027 0.002 TYR E 141 PHE 0.020 0.001 PHE R 375 TRP 0.015 0.001 TRP A 14 HIS 0.025 0.002 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8972) covalent geometry : angle 0.66392 (12182) hydrogen bonds : bond 0.03679 ( 422) hydrogen bonds : angle 4.82869 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.7024 (t60) cc_final: 0.6797 (t60) REVERT: B 75 PHE cc_start: 0.7679 (m-80) cc_final: 0.6909 (m-80) REVERT: B 220 VAL cc_start: 0.7915 (t) cc_final: 0.7692 (m) REVERT: C 156 PHE cc_start: 0.7363 (t80) cc_final: 0.7138 (t80) REVERT: C 185 LEU cc_start: 0.8185 (tp) cc_final: 0.7867 (tp) REVERT: E 186 ASP cc_start: 0.9075 (m-30) cc_final: 0.8742 (p0) REVERT: R 224 MET cc_start: 0.6449 (ptm) cc_final: 0.5719 (mmm) REVERT: R 302 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6900 (mm-30) outliers start: 23 outliers final: 19 residues processed: 122 average time/residue: 0.0894 time to fit residues: 15.5947 Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 454 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.148837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108068 restraints weight = 21480.155| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.55 r_work: 0.3469 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8972 Z= 0.137 Angle : 0.659 10.763 12182 Z= 0.332 Chirality : 0.043 0.236 1387 Planarity : 0.004 0.044 1517 Dihedral : 4.744 43.446 1216 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 2.29 % Allowed : 16.34 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1076 helix: 1.02 (0.29), residues: 294 sheet: 0.72 (0.29), residues: 332 loop : -0.59 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 282 TYR 0.030 0.002 TYR E 174 PHE 0.020 0.001 PHE R 375 TRP 0.014 0.001 TRP A 14 HIS 0.024 0.002 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8972) covalent geometry : angle 0.65922 (12182) hydrogen bonds : bond 0.03739 ( 422) hydrogen bonds : angle 4.73344 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.96 seconds wall clock time: 49 minutes 2.81 seconds (2942.81 seconds total)