Starting phenix.real_space_refine on Fri Aug 22 17:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge2_29953/08_2025/8ge2_29953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge2_29953/08_2025/8ge2_29953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ge2_29953/08_2025/8ge2_29953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge2_29953/08_2025/8ge2_29953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ge2_29953/08_2025/8ge2_29953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge2_29953/08_2025/8ge2_29953.map" } resolution = 3.3 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= -0.001 sd= 0.035 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 40 5.16 5 C 4174 2.51 5 N 1136 2.21 5 O 1123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6473 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1679 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 4, 'GLU:plan': 16, 'GLN:plan1': 4, 'ASP:plan': 13, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2349 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 5, 'TRANS': 327} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 149 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 356 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2074 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 9, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 5, 'ARG:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.27 Number of scatterers: 6473 At special positions: 0 Unit cell: (72.08, 97.52, 127.2, 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 40 16.00 O 1123 8.00 N 1136 7.00 C 4174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 388.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 48.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.107A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.589A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.855A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.592A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.573A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.642A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.653A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.041A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.903A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 237 removed outlier: 5.114A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 269 through 299 removed outlier: 4.445A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.452A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.345A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.967A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.008A 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: 3.612A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.561A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.504A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.625A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.949A 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: 3.577A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1164 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: 1.03 Time building geometry restraints manager: 0.79 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: 2103 1.34 - 1.46: 1519 1.46 - 1.58: 2936 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6614 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.322 0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 8930 1.45 - 2.89: 90 2.89 - 4.34: 16 4.34 - 5.78: 8 5.78 - 7.23: 1 Bond angle restraints: 9045 Sorted by residual: angle pdb=" CA LEU R 144 " pdb=" CB LEU R 144 " pdb=" CG LEU R 144 " ideal model delta sigma weight residual 116.30 123.53 -7.23 3.50e+00 8.16e-02 4.26e+00 angle pdb=" N GLN R 231 " pdb=" CA GLN R 231 " pdb=" CB GLN R 231 " ideal model delta sigma weight residual 110.16 112.88 -2.72 1.48e+00 4.57e-01 3.37e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.97 -5.34 3.00e+00 1.11e-01 3.17e+00 angle pdb=" C GLY A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 122.08 124.65 -2.57 1.47e+00 4.63e-01 3.05e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.30 112.83 -2.53 1.54e+00 4.22e-01 2.70e+00 ... (remaining 9040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3481 16.18 - 32.35: 272 32.35 - 48.53: 56 48.53 - 64.71: 7 64.71 - 80.88: 4 Dihedral angle restraints: 3820 sinusoidal: 1172 harmonic: 2648 Sorted by residual: 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 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LEU R 144 " pdb=" C LEU R 144 " pdb=" N LEU R 145 " pdb=" CA LEU R 145 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CG LYS B 209 " pdb=" CD LYS B 209 " pdb=" CE LYS B 209 " pdb=" NZ LYS B 209 " ideal model delta sinusoidal sigma weight residual 180.00 127.61 52.39 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 3817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 738 0.034 - 0.069: 240 0.069 - 0.103: 75 0.103 - 0.138: 26 0.138 - 0.172: 1 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE G 25 " pdb=" N ILE G 25 " pdb=" C ILE G 25 " pdb=" CB ILE G 25 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1077 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.06e+00 pdb=" C ILE R 205 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.009 2.00e-02 2.50e+03 7.38e-03 1.09e+00 pdb=" CG TYR B 59 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.87e-01 pdb=" N PRO R 168 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " 0.012 5.00e-02 4.00e+02 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 557 2.74 - 3.28: 6407 3.28 - 3.82: 10944 3.82 - 4.36: 11903 4.36 - 4.90: 22109 Nonbonded interactions: 51920 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR R 98 " pdb=" O THR R 189 " model vdw 2.295 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.314 3.040 nonbonded pdb=" O ARG A 283 " pdb=" OG1 THR A 284 " model vdw 2.332 3.040 nonbonded pdb=" NE2 GLN A 19 " pdb=" OD2 ASP B 83 " model vdw 2.338 3.120 ... (remaining 51915 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.053 6615 Z= 0.135 Angle : 0.451 7.228 9047 Z= 0.238 Chirality : 0.040 0.172 1080 Planarity : 0.003 0.029 1143 Dihedral : 12.658 80.883 2097 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.28), residues: 892 helix: 2.55 (0.26), residues: 392 sheet: 0.34 (0.38), residues: 167 loop : -0.28 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.018 0.001 TYR B 59 PHE 0.010 0.001 PHE B 234 TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6614) covalent geometry : angle 0.45095 ( 9045) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.74889 ( 2) hydrogen bonds : bond 0.16339 ( 398) hydrogen bonds : angle 6.11310 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 278 ASN cc_start: 0.9113 (m-40) cc_final: 0.8857 (m-40) REVERT: B 147 SER cc_start: 0.8963 (m) cc_final: 0.8699 (m) REVERT: B 175 GLN cc_start: 0.8308 (pm20) cc_final: 0.8038 (pm20) REVERT: B 259 GLN cc_start: 0.8241 (pt0) cc_final: 0.8024 (pt0) REVERT: R 111 SER cc_start: 0.8965 (m) cc_final: 0.8726 (m) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0741 time to fit residues: 11.1521 Evaluate side-chains 86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN G 18 GLN ** R 322 ASN ** 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 = 0.3474 r_free = 0.3474 target = 0.114613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094739 restraints weight = 10881.531| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.74 r_work: 0.3072 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6615 Z= 0.133 Angle : 0.484 7.348 9047 Z= 0.259 Chirality : 0.041 0.141 1080 Planarity : 0.003 0.028 1143 Dihedral : 3.891 17.329 981 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.54 % Allowed : 10.31 % Favored : 89.15 % 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 aren not related in a simple way. whole: 1.76 (0.29), residues: 892 helix: 2.64 (0.26), residues: 400 sheet: 0.43 (0.38), residues: 172 loop : -0.30 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.021 0.001 TYR B 59 PHE 0.010 0.001 PHE R 240 TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6614) covalent geometry : angle 0.48364 ( 9045) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.36882 ( 2) hydrogen bonds : bond 0.04165 ( 398) hydrogen bonds : angle 4.42699 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.8894 (t0) cc_final: 0.8683 (t0) REVERT: A 343 ASP cc_start: 0.8701 (m-30) cc_final: 0.8456 (m-30) REVERT: R 111 SER cc_start: 0.8805 (m) cc_final: 0.8567 (m) REVERT: R 293 ASN cc_start: 0.7447 (t0) cc_final: 0.7143 (t0) outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.0734 time to fit residues: 9.7481 Evaluate side-chains 85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094634 restraints weight = 10826.749| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.72 r_work: 0.3066 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6615 Z= 0.128 Angle : 0.460 6.491 9047 Z= 0.246 Chirality : 0.041 0.136 1080 Planarity : 0.003 0.022 1143 Dihedral : 3.868 16.891 981 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.35 % Allowed : 12.12 % Favored : 85.53 % 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 aren not related in a simple way. whole: 1.79 (0.29), residues: 892 helix: 2.68 (0.26), residues: 401 sheet: 0.38 (0.37), residues: 172 loop : -0.28 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.019 0.001 TYR B 59 PHE 0.009 0.001 PHE B 241 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6614) covalent geometry : angle 0.46005 ( 9045) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.33142 ( 2) hydrogen bonds : bond 0.03818 ( 398) hydrogen bonds : angle 4.07676 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.272 Fit side-chains REVERT: A 23 ASN cc_start: 0.8973 (t0) cc_final: 0.8746 (t0) REVERT: A 343 ASP cc_start: 0.8827 (m-30) cc_final: 0.8480 (m-30) REVERT: G 48 ASP cc_start: 0.8722 (t0) cc_final: 0.8438 (t0) REVERT: R 111 SER cc_start: 0.8799 (m) cc_final: 0.8586 (m) REVERT: R 172 HIS cc_start: 0.8350 (m-70) cc_final: 0.7542 (m90) REVERT: R 175 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7741 (mtt90) REVERT: R 228 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7711 (ttp-110) REVERT: R 293 ASN cc_start: 0.7527 (t0) cc_final: 0.7184 (t0) outliers start: 13 outliers final: 7 residues processed: 104 average time/residue: 0.0761 time to fit residues: 11.0187 Evaluate side-chains 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** R 322 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094595 restraints weight = 10908.583| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.74 r_work: 0.3073 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6615 Z= 0.124 Angle : 0.455 6.856 9047 Z= 0.243 Chirality : 0.041 0.145 1080 Planarity : 0.003 0.022 1143 Dihedral : 3.834 17.362 981 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.71 % Allowed : 13.02 % Favored : 84.27 % 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 aren not related in a simple way. whole: 1.81 (0.29), residues: 892 helix: 2.62 (0.26), residues: 408 sheet: 0.48 (0.39), residues: 159 loop : -0.25 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.016 0.001 TYR B 59 PHE 0.009 0.001 PHE R 289 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6614) covalent geometry : angle 0.45540 ( 9045) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.25453 ( 2) hydrogen bonds : bond 0.03701 ( 398) hydrogen bonds : angle 3.98596 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.263 Fit side-chains REVERT: A 23 ASN cc_start: 0.8986 (t0) cc_final: 0.8767 (t0) REVERT: A 343 ASP cc_start: 0.8817 (m-30) cc_final: 0.8331 (m-30) REVERT: G 48 ASP cc_start: 0.8735 (t0) cc_final: 0.8448 (t0) REVERT: R 228 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7613 (ttp-110) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.0772 time to fit residues: 10.7358 Evaluate side-chains 96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 322 ASN ** 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 = 0.3485 r_free = 0.3485 target = 0.115166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095335 restraints weight = 10982.847| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.72 r_work: 0.3086 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6615 Z= 0.112 Angle : 0.448 7.234 9047 Z= 0.238 Chirality : 0.041 0.146 1080 Planarity : 0.003 0.034 1143 Dihedral : 3.792 17.722 981 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.71 % Allowed : 14.29 % Favored : 83.00 % 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 aren not related in a simple way. whole: 1.88 (0.29), residues: 892 helix: 2.73 (0.25), residues: 403 sheet: 0.44 (0.38), residues: 159 loop : -0.21 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.015 0.001 TYR A 253 PHE 0.008 0.001 PHE R 289 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 172 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6614) covalent geometry : angle 0.44820 ( 9045) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.27373 ( 2) hydrogen bonds : bond 0.03518 ( 398) hydrogen bonds : angle 3.88243 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.268 Fit side-chains REVERT: A 23 ASN cc_start: 0.9006 (t0) cc_final: 0.8770 (t0) REVERT: A 343 ASP cc_start: 0.8804 (m-30) cc_final: 0.8326 (m-30) REVERT: G 48 ASP cc_start: 0.8711 (t0) cc_final: 0.8426 (t0) REVERT: R 228 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7643 (ttp-110) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.0797 time to fit residues: 11.5490 Evaluate side-chains 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 322 ASN ** 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 = 0.3406 r_free = 0.3406 target = 0.109489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.089721 restraints weight = 11171.064| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.71 r_work: 0.2991 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6615 Z= 0.285 Angle : 0.570 6.720 9047 Z= 0.307 Chirality : 0.045 0.155 1080 Planarity : 0.003 0.034 1143 Dihedral : 4.292 16.337 981 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.62 % Allowed : 15.01 % 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 aren not related in a simple way. whole: 1.58 (0.29), residues: 892 helix: 2.54 (0.26), residues: 395 sheet: 0.06 (0.36), residues: 184 loop : -0.24 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.028 0.002 TYR B 59 PHE 0.021 0.002 PHE R 289 TRP 0.014 0.001 TRP B 339 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00679 ( 6614) covalent geometry : angle 0.57003 ( 9045) SS BOND : bond 0.00391 ( 1) SS BOND : angle 0.13639 ( 2) hydrogen bonds : bond 0.04606 ( 398) hydrogen bonds : angle 4.21236 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.260 Fit side-chains REVERT: A 343 ASP cc_start: 0.8957 (m-30) cc_final: 0.8473 (m-30) REVERT: B 175 GLN cc_start: 0.8265 (pm20) cc_final: 0.7964 (pm20) REVERT: B 189 SER cc_start: 0.9001 (p) cc_final: 0.8795 (m) REVERT: B 262 MET cc_start: 0.8511 (mtp) cc_final: 0.8195 (mtp) REVERT: G 48 ASP cc_start: 0.8859 (t0) cc_final: 0.8557 (t0) REVERT: G 50 LEU cc_start: 0.8551 (mt) cc_final: 0.8350 (mt) outliers start: 20 outliers final: 16 residues processed: 98 average time/residue: 0.0775 time to fit residues: 10.4191 Evaluate side-chains 93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093309 restraints weight = 10892.784| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.73 r_work: 0.3053 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6615 Z= 0.122 Angle : 0.467 8.077 9047 Z= 0.247 Chirality : 0.041 0.137 1080 Planarity : 0.003 0.029 1143 Dihedral : 3.958 16.534 981 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.44 % Allowed : 15.73 % Favored : 80.83 % 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 aren not related in a simple way. whole: 1.65 (0.29), residues: 892 helix: 2.51 (0.26), residues: 408 sheet: 0.21 (0.39), residues: 157 loop : -0.26 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.016 0.001 TYR A 253 PHE 0.009 0.001 PHE R 290 TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS R 172 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6614) covalent geometry : angle 0.46731 ( 9045) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.03983 ( 2) hydrogen bonds : bond 0.03745 ( 398) hydrogen bonds : angle 3.99930 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.261 Fit side-chains REVERT: A 343 ASP cc_start: 0.8872 (m-30) cc_final: 0.8444 (m-30) REVERT: B 59 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: B 175 GLN cc_start: 0.8232 (pm20) cc_final: 0.7943 (pm20) REVERT: B 232 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8799 (tp) REVERT: B 262 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7984 (mtp) REVERT: G 48 ASP cc_start: 0.8806 (t0) cc_final: 0.8496 (t0) REVERT: R 228 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7637 (ttp-110) outliers start: 19 outliers final: 13 residues processed: 102 average time/residue: 0.0769 time to fit residues: 10.9297 Evaluate side-chains 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094824 restraints weight = 10984.859| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.75 r_work: 0.3075 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6615 Z= 0.106 Angle : 0.454 8.328 9047 Z= 0.239 Chirality : 0.041 0.134 1080 Planarity : 0.003 0.026 1143 Dihedral : 3.795 17.757 981 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.80 % Allowed : 16.46 % Favored : 79.75 % 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 aren not related in a simple way. whole: 1.79 (0.29), residues: 892 helix: 2.67 (0.26), residues: 407 sheet: 0.45 (0.39), residues: 159 loop : -0.34 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 175 TYR 0.017 0.001 TYR A 253 PHE 0.008 0.001 PHE R 290 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 172 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6614) covalent geometry : angle 0.45419 ( 9045) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.22479 ( 2) hydrogen bonds : bond 0.03527 ( 398) hydrogen bonds : angle 3.89079 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.292 Fit side-chains REVERT: A 343 ASP cc_start: 0.8813 (m-30) cc_final: 0.8393 (m-30) REVERT: B 59 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: B 175 GLN cc_start: 0.8285 (pm20) cc_final: 0.8000 (pm20) REVERT: B 232 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8771 (tp) REVERT: B 259 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: B 262 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7974 (mtp) REVERT: R 228 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7678 (ttp-110) outliers start: 21 outliers final: 12 residues processed: 104 average time/residue: 0.0755 time to fit residues: 10.9324 Evaluate side-chains 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095608 restraints weight = 11028.974| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.73 r_work: 0.3083 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6615 Z= 0.104 Angle : 0.456 8.356 9047 Z= 0.238 Chirality : 0.041 0.171 1080 Planarity : 0.003 0.026 1143 Dihedral : 3.721 17.963 981 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.25 % Allowed : 17.54 % Favored : 79.20 % 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 aren not related in a simple way. whole: 1.86 (0.29), residues: 892 helix: 2.81 (0.26), residues: 402 sheet: 0.44 (0.38), residues: 159 loop : -0.34 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.018 0.001 TYR A 253 PHE 0.008 0.001 PHE B 241 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6614) covalent geometry : angle 0.45645 ( 9045) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.26184 ( 2) hydrogen bonds : bond 0.03458 ( 398) hydrogen bonds : angle 3.86507 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.251 Fit side-chains REVERT: A 343 ASP cc_start: 0.8818 (m-30) cc_final: 0.8397 (m-30) REVERT: B 59 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 175 GLN cc_start: 0.8277 (pm20) cc_final: 0.8004 (pm20) REVERT: B 232 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8778 (tp) REVERT: B 259 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: B 262 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7990 (mtp) REVERT: G 48 ASP cc_start: 0.8737 (t0) cc_final: 0.8453 (t0) REVERT: R 228 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7700 (ttp-110) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 0.0704 time to fit residues: 9.9179 Evaluate side-chains 100 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096135 restraints weight = 10832.555| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.70 r_work: 0.3091 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6615 Z= 0.105 Angle : 0.458 8.419 9047 Z= 0.240 Chirality : 0.041 0.185 1080 Planarity : 0.003 0.030 1143 Dihedral : 3.682 18.213 981 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.44 % Allowed : 17.90 % Favored : 78.66 % 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 aren not related in a simple way. whole: 1.87 (0.29), residues: 892 helix: 2.82 (0.26), residues: 397 sheet: 0.40 (0.37), residues: 165 loop : -0.29 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 175 TYR 0.018 0.001 TYR A 253 PHE 0.008 0.001 PHE B 241 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6614) covalent geometry : angle 0.45804 ( 9045) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.27346 ( 2) hydrogen bonds : bond 0.03473 ( 398) hydrogen bonds : angle 3.84955 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.267 Fit side-chains REVERT: A 343 ASP cc_start: 0.8812 (m-30) cc_final: 0.8387 (m-30) REVERT: B 59 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 175 GLN cc_start: 0.8254 (pm20) cc_final: 0.7978 (pm20) REVERT: B 232 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8784 (tp) REVERT: B 259 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: B 262 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7960 (mtp) REVERT: R 228 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7630 (ttp-110) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 0.0737 time to fit residues: 10.2773 Evaluate side-chains 98 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 294 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094859 restraints weight = 11044.988| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.73 r_work: 0.3071 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6615 Z= 0.122 Angle : 0.466 8.258 9047 Z= 0.243 Chirality : 0.041 0.178 1080 Planarity : 0.003 0.027 1143 Dihedral : 3.737 17.745 981 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.44 % Allowed : 17.72 % Favored : 78.84 % 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 aren not related in a simple way. whole: 1.90 (0.29), residues: 892 helix: 2.80 (0.26), residues: 402 sheet: 0.37 (0.37), residues: 167 loop : -0.23 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 175 TYR 0.019 0.001 TYR A 253 PHE 0.009 0.001 PHE B 241 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 172 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6614) covalent geometry : angle 0.46564 ( 9045) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.24352 ( 2) hydrogen bonds : bond 0.03588 ( 398) hydrogen bonds : angle 3.86016 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1454.51 seconds wall clock time: 25 minutes 47.09 seconds (1547.09 seconds total)