Starting phenix.real_space_refine on Fri Sep 11 16:17:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25hw_80125/09_2026/25hw_80125.cif Found real_map, /net/cci-nas-00/data/ceres_data/25hw_80125/09_2026/25hw_80125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25hw_80125/09_2026/25hw_80125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25hw_80125/09_2026/25hw_80125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25hw_80125/09_2026/25hw_80125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25hw_80125/09_2026/25hw_80125.map" } resolution = 3.28 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= 0.007 sd= 0.021 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 42 5.16 5 C 6420 2.51 5 N 1754 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9980 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "E" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 727 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1583 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 186} Chain: "A" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2777 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 4203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4203 Classifications: {'peptide': 548} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 516} Chain breaks: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.22 Number of scatterers: 9980 At special positions: 0 Unit cell: (90.72, 136.08, 157.08, 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 42 16.00 O 1764 8.00 N 1754 7.00 C 6420 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: 0.80 Conformation dependent library (CDL) restraints added in 315.6 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 51.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 13 through 69 removed outlier: 4.196A pdb=" N THR D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.569A pdb=" N LEU D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 26 Processing helix chain 'E' and resid 30 through 68 removed outlier: 3.822A pdb=" N VAL E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.562A pdb=" N GLU E 73 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.693A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 removed outlier: 4.001A pdb=" N MET C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.802A pdb=" N GLU C 173 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 233 through 249 Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.755A pdb=" N LEU A 25 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 56 through 77 removed outlier: 4.098A pdb=" N ARG A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.767A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.718A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 200 through 218 removed outlier: 3.741A pdb=" N VAL A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 removed outlier: 3.680A pdb=" N GLY A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.502A pdb=" N VAL A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.883A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.510A pdb=" N LEU A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.702A pdb=" N PHE A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 381 Processing helix chain 'B' and resid 15 through 39 removed outlier: 3.888A pdb=" N HIS B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 224 through 243 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.902A pdb=" N SER B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.807A pdb=" N ILE B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.503A pdb=" N TYR B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 4.140A pdb=" N TYR B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.968A pdb=" N LEU B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.851A pdb=" N VAL B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 553 removed outlier: 4.190A pdb=" N VAL B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Proline residue: B 540 - end of helix removed outlier: 3.592A pdb=" N MET B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.164A pdb=" N GLU C 226 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU C 226 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR C 221 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLN C 228 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 219 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 218 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU C 209 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 220 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 150 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 84 removed outlier: 5.658A pdb=" N SER C 82 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 142 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C 84 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU C 144 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS C 127 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 58 removed outlier: 6.541A pdb=" N LEU B 196 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP B 206 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 123 through 129 removed outlier: 6.343A pdb=" N LEU B 125 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA B 84 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG B 127 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU B 82 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 259 through 265 removed outlier: 5.995A pdb=" N ILE B 259 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 253 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 249 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 247 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 518 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 506 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 508 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 316 through 317 removed outlier: 4.037A pdb=" N VAL B 316 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 340 " --> pdb=" O VAL B 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 430 through 431 removed outlier: 3.600A pdb=" N VAL B 446 " --> pdb=" O SER B 431 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1455 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: 1.46 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3267 1.34 - 1.46: 1406 1.46 - 1.57: 5439 1.57 - 1.69: 1 1.69 - 1.81: 77 Bond restraints: 10190 Sorted by residual: bond pdb=" CB PRO B 398 " pdb=" CG PRO B 398 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" C SER A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.14e+00 bond pdb=" C PHE A 8 " pdb=" N PRO A 9 " ideal model delta sigma weight residual 1.334 1.355 -0.022 2.34e-02 1.83e+03 8.49e-01 bond pdb=" CB LYS E 67 " pdb=" CG LYS E 67 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.13e-01 bond pdb=" C ILE A 18 " pdb=" O ILE A 18 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.95e-01 ... (remaining 10185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 13527 1.49 - 2.98: 225 2.98 - 4.47: 52 4.47 - 5.96: 13 5.96 - 7.45: 4 Bond angle restraints: 13821 Sorted by residual: angle pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" CD PRO B 398 " ideal model delta sigma weight residual 112.00 105.38 6.62 1.40e+00 5.10e-01 2.24e+01 angle pdb=" N GLN B 372 " pdb=" CA GLN B 372 " pdb=" CB GLN B 372 " ideal model delta sigma weight residual 110.16 114.88 -4.72 1.48e+00 4.57e-01 1.02e+01 angle pdb=" CA ILE A 18 " pdb=" C ILE A 18 " pdb=" N ASP A 19 " ideal model delta sigma weight residual 116.60 120.26 -3.66 1.45e+00 4.76e-01 6.39e+00 angle pdb=" N GLY E 27 " pdb=" CA GLY E 27 " pdb=" C GLY E 27 " ideal model delta sigma weight residual 110.46 114.02 -3.56 1.43e+00 4.89e-01 6.18e+00 angle pdb=" C ILE B 39 " pdb=" N ASP B 40 " pdb=" CA ASP B 40 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.68e+00 ... (remaining 13816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5422 17.58 - 35.17: 510 35.17 - 52.75: 97 52.75 - 70.34: 11 70.34 - 87.92: 15 Dihedral angle restraints: 6055 sinusoidal: 2406 harmonic: 3649 Sorted by residual: dihedral pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" N PHE C 108 " pdb=" CA PHE C 108 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ILE B 325 " pdb=" C ILE B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR A 240 " pdb=" C TYR A 240 " pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta harmonic sigma weight residual -180.00 -163.92 -16.08 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1136 0.039 - 0.078: 316 0.078 - 0.116: 97 0.116 - 0.155: 11 0.155 - 0.194: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CB THR C 165 " pdb=" CA THR C 165 " pdb=" OG1 THR C 165 " pdb=" CG2 THR C 165 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA VAL A 149 " pdb=" N VAL A 149 " pdb=" C VAL A 149 " pdb=" CB VAL A 149 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA GLN B 372 " pdb=" N GLN B 372 " pdb=" C GLN B 372 " pdb=" CB GLN B 372 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1558 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 397 " -0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 398 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 10 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 11 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 11 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 12 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " -0.019 5.00e-02 4.00e+02 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 432 2.73 - 3.27: 9876 3.27 - 3.81: 16184 3.81 - 4.36: 17541 4.36 - 4.90: 31130 Nonbonded interactions: 75163 Sorted by model distance: nonbonded pdb=" O GLY B 534 " pdb=" OG SER B 538 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLN B 324 " pdb=" OG1 THR B 329 " model vdw 2.193 3.040 nonbonded pdb=" OG SER B 334 " pdb=" OG SER B 337 " model vdw 2.214 3.040 nonbonded pdb=" O GLY E 27 " pdb=" OG SER E 30 " model vdw 2.283 3.040 nonbonded pdb=" ND2 ASN C 158 " pdb=" OE1 GLN C 160 " model vdw 2.303 3.120 ... (remaining 75158 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.770 Find NCS groups from input model: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.002 0.108 10190 Z= 0.094 Angle : 0.509 7.445 13821 Z= 0.260 Chirality : 0.039 0.194 1561 Planarity : 0.004 0.102 1770 Dihedral : 14.346 87.920 3721 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.63 (0.25), residues: 1270 helix: 2.26 (0.23), residues: 592 sheet: 0.55 (0.60), residues: 82 loop : -1.63 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.007 0.001 TYR B 407 PHE 0.023 0.001 PHE A 334 TRP 0.006 0.001 TRP B 310 HIS 0.002 0.000 HIS B 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (10190) covalent geometry : angle 0.50897 / 0.26 (13821) hydrogen bonds : bond 0.16596 / 11.52 ( 499) hydrogen bonds : angle 6.26728 / 4.48 ( 1455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.5639 (ptt) cc_final: 0.3755 (tpt) REVERT: B 36 LEU cc_start: 0.6638 (tt) cc_final: 0.5964 (mm) REVERT: B 546 MET cc_start: 0.8608 (tpt) cc_final: 0.8076 (tpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0969 time to fit residues: 17.9959 Evaluate side-chains 99 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0970 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 GLN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 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 = 0.4286 r_free = 0.4286 target = 0.119996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.097368 restraints weight = 31382.264| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.54 r_work: 0.3681 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10190 Z= 0.166 Angle : 0.587 9.560 13821 Z= 0.299 Chirality : 0.043 0.147 1561 Planarity : 0.005 0.059 1770 Dihedral : 3.854 21.951 1402 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.68 % Allowed : 9.84 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.15 (0.24), residues: 1270 helix: 1.72 (0.22), residues: 617 sheet: -0.26 (0.53), residues: 101 loop : -1.80 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 200 TYR 0.015 0.002 TYR A 324 PHE 0.022 0.002 PHE A 297 TRP 0.012 0.001 TRP D 36 HIS 0.008 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (10190) covalent geometry : angle 0.58732 / 0.30 (13821) hydrogen bonds : bond 0.04131 / 2.68 ( 499) hydrogen bonds : angle 4.62670 / 3.33 ( 1455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5390 (ptt) cc_final: 0.3662 (tpt) REVERT: A 381 THR cc_start: 0.6789 (t) cc_final: 0.6388 (p) REVERT: B 54 ARG cc_start: 0.6637 (mtm180) cc_final: 0.5993 (mtm-85) REVERT: B 348 LYS cc_start: 0.8780 (tttp) cc_final: 0.8504 (tttp) REVERT: B 351 ASN cc_start: 0.6200 (t0) cc_final: 0.5980 (t0) REVERT: B 546 MET cc_start: 0.8763 (tpt) cc_final: 0.8514 (tpp) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.1099 time to fit residues: 18.9644 Evaluate side-chains 112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 251 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 91 GLN C 255 ASN B 194 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.117272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.091968 restraints weight = 31895.481| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.50 r_work: 0.3555 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10190 Z= 0.184 Angle : 0.606 8.418 13821 Z= 0.308 Chirality : 0.042 0.141 1561 Planarity : 0.004 0.051 1770 Dihedral : 4.127 20.284 1402 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.45 % Allowed : 14.18 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.11 (0.24), residues: 1270 helix: 1.50 (0.21), residues: 616 sheet: -0.48 (0.52), residues: 102 loop : -1.90 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 374 TYR 0.029 0.002 TYR A 324 PHE 0.016 0.002 PHE B 383 TRP 0.009 0.001 TRP C 271 HIS 0.005 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (10190) covalent geometry : angle 0.60604 / 0.31 (13821) hydrogen bonds : bond 0.04628 / 3.04 ( 499) hydrogen bonds : angle 4.47869 / 3.20 ( 1455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 132 ARG cc_start: 0.5005 (OUTLIER) cc_final: 0.4646 (ptm-80) REVERT: C 212 SER cc_start: 0.7580 (m) cc_final: 0.7282 (p) REVERT: A 114 MET cc_start: 0.5378 (ptt) cc_final: 0.3510 (tpt) REVERT: A 169 LEU cc_start: 0.5865 (tp) cc_final: 0.5551 (mt) REVERT: A 324 TYR cc_start: 0.7628 (m-80) cc_final: 0.7410 (m-80) REVERT: A 381 THR cc_start: 0.6943 (t) cc_final: 0.6492 (p) REVERT: B 54 ARG cc_start: 0.6752 (mtm180) cc_final: 0.6207 (mtm-85) REVERT: B 351 ASN cc_start: 0.6289 (t0) cc_final: 0.6048 (t0) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.1078 time to fit residues: 20.6244 Evaluate side-chains 123 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 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 = 0.4284 r_free = 0.4284 target = 0.126202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.101769 restraints weight = 32847.070| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.35 r_work: 0.3561 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10190 Z= 0.118 Angle : 0.545 7.771 13821 Z= 0.275 Chirality : 0.040 0.142 1561 Planarity : 0.004 0.050 1770 Dihedral : 3.858 20.086 1402 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.54 % Allowed : 15.72 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.02 (0.24), residues: 1270 helix: 1.64 (0.21), residues: 622 sheet: -0.57 (0.52), residues: 102 loop : -1.97 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.022 0.001 TYR A 324 PHE 0.016 0.001 PHE B 533 TRP 0.006 0.001 TRP C 217 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10190) covalent geometry : angle 0.54496 / 0.27 (13821) hydrogen bonds : bond 0.03820 / 2.50 ( 499) hydrogen bonds : angle 4.25409 / 3.06 ( 1455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: E 67 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8063 (ttmm) REVERT: C 132 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4642 (ptm-80) REVERT: C 212 SER cc_start: 0.7545 (m) cc_final: 0.7259 (p) REVERT: A 114 MET cc_start: 0.5280 (ptt) cc_final: 0.3497 (tpt) REVERT: A 169 LEU cc_start: 0.5891 (tp) cc_final: 0.5596 (mt) REVERT: A 203 MET cc_start: 0.0637 (OUTLIER) cc_final: -0.0005 (tpt) REVERT: A 324 TYR cc_start: 0.7623 (m-80) cc_final: 0.7341 (m-80) REVERT: B 54 ARG cc_start: 0.6684 (mtm180) cc_final: 0.6247 (mtm-85) REVERT: B 348 LYS cc_start: 0.8753 (tttp) cc_final: 0.8460 (tppt) REVERT: B 351 ASN cc_start: 0.6214 (t0) cc_final: 0.5990 (t0) REVERT: B 375 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7189 (mp) REVERT: B 554 ASN cc_start: 0.7865 (t0) cc_final: 0.7151 (p0) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.0987 time to fit residues: 18.7055 Evaluate side-chains 121 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 524 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 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 = 0.4293 r_free = 0.4293 target = 0.126960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.103518 restraints weight = 32432.625| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.27 r_work: 0.3580 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10190 Z= 0.105 Angle : 0.524 8.407 13821 Z= 0.263 Chirality : 0.039 0.162 1561 Planarity : 0.004 0.050 1770 Dihedral : 3.680 19.196 1402 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.74 % Allowed : 16.49 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.15 (0.24), residues: 1270 helix: 1.85 (0.21), residues: 621 sheet: -0.58 (0.53), residues: 100 loop : -1.95 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 374 TYR 0.020 0.001 TYR A 324 PHE 0.014 0.001 PHE B 533 TRP 0.011 0.001 TRP C 271 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (10190) covalent geometry : angle 0.52367 / 0.26 (13821) hydrogen bonds : bond 0.03457 / 2.28 ( 499) hydrogen bonds : angle 4.06424 / 2.93 ( 1455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 67 LYS cc_start: 0.8297 (tmmt) cc_final: 0.7978 (ttmm) REVERT: A 114 MET cc_start: 0.5162 (ptt) cc_final: 0.3459 (tpt) REVERT: A 169 LEU cc_start: 0.5799 (tp) cc_final: 0.5394 (mt) REVERT: A 203 MET cc_start: 0.0790 (OUTLIER) cc_final: 0.0249 (tpt) REVERT: B 54 ARG cc_start: 0.6607 (mtm180) cc_final: 0.6201 (mtm-85) REVERT: B 277 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 348 LYS cc_start: 0.8776 (tttp) cc_final: 0.8503 (tppt) REVERT: B 375 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6992 (mp) REVERT: B 554 ASN cc_start: 0.7795 (t0) cc_final: 0.7127 (p0) outliers start: 18 outliers final: 12 residues processed: 132 average time/residue: 0.0985 time to fit residues: 18.8118 Evaluate side-chains 129 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.123563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.098835 restraints weight = 32834.090| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.36 r_work: 0.3521 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10190 Z= 0.180 Angle : 0.611 7.786 13821 Z= 0.310 Chirality : 0.042 0.137 1561 Planarity : 0.004 0.051 1770 Dihedral : 4.150 18.906 1402 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.80 % Allowed : 16.30 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.13 (0.24), residues: 1270 helix: 1.61 (0.21), residues: 613 sheet: -0.95 (0.48), residues: 109 loop : -1.97 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 374 TYR 0.029 0.002 TYR A 324 PHE 0.016 0.002 PHE A 334 TRP 0.012 0.001 TRP C 271 HIS 0.005 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (10190) covalent geometry : angle 0.61113 / 0.31 (13821) hydrogen bonds : bond 0.04464 / 2.95 ( 499) hydrogen bonds : angle 4.34843 / 3.12 ( 1455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 67 LYS cc_start: 0.8415 (tmmt) cc_final: 0.8136 (ttmm) REVERT: C 212 SER cc_start: 0.7487 (m) cc_final: 0.7211 (p) REVERT: A 114 MET cc_start: 0.5160 (ptt) cc_final: 0.3361 (tpt) REVERT: A 175 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: B 54 ARG cc_start: 0.6867 (mtm180) cc_final: 0.6643 (mtm-85) REVERT: B 375 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7315 (mp) REVERT: B 546 MET cc_start: 0.8554 (tpt) cc_final: 0.8147 (tpp) REVERT: B 554 ASN cc_start: 0.8024 (t0) cc_final: 0.7285 (p0) outliers start: 29 outliers final: 17 residues processed: 146 average time/residue: 0.1042 time to fit residues: 21.5922 Evaluate side-chains 136 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 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 = 0.4276 r_free = 0.4276 target = 0.125376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.101097 restraints weight = 32576.483| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.36 r_work: 0.3578 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10190 Z= 0.114 Angle : 0.578 9.571 13821 Z= 0.288 Chirality : 0.041 0.196 1561 Planarity : 0.004 0.052 1770 Dihedral : 3.869 19.176 1402 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.93 % Allowed : 19.19 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.01 (0.24), residues: 1270 helix: 1.72 (0.21), residues: 616 sheet: -0.84 (0.51), residues: 102 loop : -1.94 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 489 TYR 0.031 0.001 TYR A 324 PHE 0.014 0.001 PHE B 533 TRP 0.013 0.001 TRP A 330 HIS 0.002 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10190) covalent geometry : angle 0.57807 / 0.29 (13821) hydrogen bonds : bond 0.03701 / 2.43 ( 499) hydrogen bonds : angle 4.14691 / 2.97 ( 1455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: E 61 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7749 (tt0) REVERT: E 67 LYS cc_start: 0.8240 (tmmt) cc_final: 0.8002 (ttmm) REVERT: E 75 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7258 (ttt90) REVERT: E 79 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7529 (mp0) REVERT: C 212 SER cc_start: 0.7555 (m) cc_final: 0.7274 (p) REVERT: A 114 MET cc_start: 0.5237 (ptt) cc_final: 0.3419 (tpt) REVERT: A 162 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7524 (m) REVERT: A 175 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: A 254 TRP cc_start: 0.7431 (m100) cc_final: 0.7224 (m100) REVERT: A 324 TYR cc_start: 0.7657 (m-80) cc_final: 0.7370 (m-80) REVERT: A 354 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6598 (m-10) REVERT: B 54 ARG cc_start: 0.6718 (mtm180) cc_final: 0.6441 (mtm-85) REVERT: B 348 LYS cc_start: 0.8825 (tttp) cc_final: 0.8622 (tptp) REVERT: B 375 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7050 (mp) REVERT: B 554 ASN cc_start: 0.7875 (t0) cc_final: 0.7235 (p0) outliers start: 20 outliers final: 13 residues processed: 139 average time/residue: 0.1064 time to fit residues: 20.9828 Evaluate side-chains 131 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 102 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 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 = 0.4273 r_free = 0.4273 target = 0.125105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100805 restraints weight = 32670.756| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.33 r_work: 0.3555 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10190 Z= 0.120 Angle : 0.588 9.262 13821 Z= 0.292 Chirality : 0.041 0.207 1561 Planarity : 0.004 0.053 1770 Dihedral : 3.819 18.982 1402 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.12 % Allowed : 19.86 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.04 (0.24), residues: 1270 helix: 1.80 (0.21), residues: 615 sheet: -0.93 (0.53), residues: 95 loop : -1.94 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 75 TYR 0.028 0.001 TYR A 324 PHE 0.013 0.001 PHE B 533 TRP 0.016 0.001 TRP C 271 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10190) covalent geometry : angle 0.58798 / 0.29 (13821) hydrogen bonds : bond 0.03652 / 2.40 ( 499) hydrogen bonds : angle 4.08529 / 2.92 ( 1455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: E 61 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7753 (tt0) REVERT: E 67 LYS cc_start: 0.8204 (tmmt) cc_final: 0.7997 (ttmm) REVERT: C 132 ARG cc_start: 0.4924 (OUTLIER) cc_final: 0.4590 (ptm-80) REVERT: A 114 MET cc_start: 0.5107 (ptt) cc_final: 0.3347 (tpt) REVERT: A 162 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7450 (m) REVERT: A 175 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: A 354 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: B 54 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6508 (mtm-85) REVERT: B 375 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7010 (mp) REVERT: B 554 ASN cc_start: 0.7832 (t0) cc_final: 0.7302 (p0) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.1031 time to fit residues: 19.4181 Evaluate side-chains 135 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** 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 = 0.4281 r_free = 0.4281 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.101688 restraints weight = 32654.244| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.56 r_work: 0.3574 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10190 Z= 0.112 Angle : 0.585 9.631 13821 Z= 0.289 Chirality : 0.040 0.171 1561 Planarity : 0.004 0.053 1770 Dihedral : 3.743 18.801 1402 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.22 % Allowed : 19.86 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.07 (0.24), residues: 1270 helix: 1.82 (0.21), residues: 621 sheet: -0.84 (0.52), residues: 100 loop : -1.97 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 199 TYR 0.028 0.001 TYR A 324 PHE 0.013 0.001 PHE B 533 TRP 0.014 0.001 TRP C 271 HIS 0.002 0.001 HIS B 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10190) covalent geometry : angle 0.58485 / 0.29 (13821) hydrogen bonds : bond 0.03498 / 2.29 ( 499) hydrogen bonds : angle 4.04714 / 2.90 ( 1455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: E 61 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7767 (tt0) REVERT: E 67 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7956 (ttmm) REVERT: E 79 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7534 (mp0) REVERT: C 132 ARG cc_start: 0.4856 (OUTLIER) cc_final: 0.4593 (ptm-80) REVERT: A 114 MET cc_start: 0.5064 (ptt) cc_final: 0.3327 (tpt) REVERT: A 162 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7415 (m) REVERT: A 175 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: A 324 TYR cc_start: 0.7626 (m-80) cc_final: 0.7385 (m-80) REVERT: A 354 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: B 375 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6935 (mp) REVERT: B 554 ASN cc_start: 0.7847 (t0) cc_final: 0.7321 (p0) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.0978 time to fit residues: 18.8949 Evaluate side-chains 136 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** 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 = 0.4281 r_free = 0.4281 target = 0.125503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.101500 restraints weight = 32484.053| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.34 r_work: 0.3583 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10190 Z= 0.114 Angle : 0.594 10.190 13821 Z= 0.295 Chirality : 0.041 0.189 1561 Planarity : 0.004 0.052 1770 Dihedral : 3.759 18.817 1402 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.22 % Allowed : 19.86 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.07 (0.24), residues: 1270 helix: 1.81 (0.21), residues: 621 sheet: -0.82 (0.53), residues: 95 loop : -1.97 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 75 TYR 0.028 0.001 TYR A 324 PHE 0.013 0.001 PHE B 533 TRP 0.014 0.001 TRP C 271 HIS 0.003 0.001 HIS B 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10190) covalent geometry : angle 0.59448 / 0.29 (13821) hydrogen bonds : bond 0.03453 / 2.27 ( 499) hydrogen bonds : angle 4.02206 / 2.88 ( 1455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: E 61 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7720 (tt0) REVERT: E 67 LYS cc_start: 0.8109 (tmmt) cc_final: 0.7908 (ttmm) REVERT: C 111 ASP cc_start: 0.5240 (t0) cc_final: 0.4891 (p0) REVERT: A 114 MET cc_start: 0.5035 (ptt) cc_final: 0.3274 (tpt) REVERT: A 175 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: A 324 TYR cc_start: 0.7571 (m-80) cc_final: 0.7326 (m-80) REVERT: A 354 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6519 (m-10) REVERT: B 375 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6952 (mp) REVERT: B 554 ASN cc_start: 0.7813 (t0) cc_final: 0.7329 (p0) outliers start: 23 outliers final: 17 residues processed: 138 average time/residue: 0.0922 time to fit residues: 18.3367 Evaluate side-chains 141 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 277 GLN ** 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 = 0.4259 r_free = 0.4259 target = 0.124177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.100389 restraints weight = 32978.331| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.30 r_work: 0.3560 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10190 Z= 0.140 Angle : 0.621 9.824 13821 Z= 0.308 Chirality : 0.041 0.159 1561 Planarity : 0.004 0.053 1770 Dihedral : 3.941 17.747 1402 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.41 % Allowed : 20.35 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.03 (0.24), residues: 1270 helix: 1.74 (0.21), residues: 616 sheet: -0.83 (0.51), residues: 102 loop : -1.90 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.026 0.001 TYR A 324 PHE 0.013 0.001 PHE B 533 TRP 0.015 0.001 TRP C 271 HIS 0.004 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10190) covalent geometry : angle 0.62098 / 0.31 (13821) hydrogen bonds : bond 0.03901 / 2.55 ( 499) hydrogen bonds : angle 4.15303 / 2.96 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.05 seconds wall clock time: 51 minutes 32.05 seconds (3092.05 seconds total)