Starting phenix.real_space_refine on Thu Jul 2 07:24:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.map" model { file = "/net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g04_29644/07_2026/8g04_29644.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 39 5.16 5 C 4664 2.51 5 N 1236 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7314 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1136 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 11, 'TRANS': 139} Chain: "B" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3027 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 34, 'TRANS': 363} Chain breaks: 5 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCA:plan-2': 1, 'HIS:plan': 3, 'GLN:plan1': 6, 'ASN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 7, 'PHE:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "C" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3001 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 34, 'TRANS': 360} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 9, 'ARG:plan': 8, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 5, 'HIS:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.72, per 1000 atoms: 0.24 Number of scatterers: 7314 At special positions: 0 Unit cell: (83.006, 116.424, 130.438, 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 39 16.00 O 1375 8.00 N 1236 7.00 C 4664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 352 " 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=6, symmetry=0 Links applied NAG-ASN " NAG B1001 " - " ASN B 117 " " NAG B1002 " - " ASN B 298 " " NAG B1003 " - " ASN B 358 " " NAG C1001 " - " ASN C 117 " " NAG C1002 " - " ASN C 298 " " NAG C1003 " - " ASN C 358 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 312.3 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 19 sheets defined 18.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 29 through 48 removed outlier: 4.057A pdb=" N LEU A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 48 " --> pdb=" O HIS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.758A pdb=" N THR A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 100 removed outlier: 3.599A pdb=" N GLY A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.615A pdb=" N SER A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.270A pdb=" N ILE A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.814A pdb=" N LEU A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.801A pdb=" N ALA B 286 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 158 through 163 removed outlier: 5.348A pdb=" N ASP C 163 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 414 through 418 removed outlier: 4.099A pdb=" N ALA C 417 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.550A pdb=" N THR B 49 " --> pdb=" O PHE B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 77 removed outlier: 4.562A pdb=" N LEU B 65 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 121 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN B 113 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR B 119 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 143 removed outlier: 3.576A pdb=" N TRP B 154 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 187 removed outlier: 4.564A pdb=" N TYR B 167 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.774A pdb=" N PHE B 292 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 300 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.696A pdb=" N SER B 310 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 333 removed outlier: 3.696A pdb=" N SER B 310 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 362 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 396 through 399 Processing sheet with id=AB1, first strand: chain 'B' and resid 436 through 438 removed outlier: 3.654A pdb=" N LYS B 436 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 428 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 463 " --> pdb=" O TRP B 474 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP B 474 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 465 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.535A pdb=" N THR C 49 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.697A pdb=" N ILE C 138 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 155 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 142 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 183 through 186 Processing sheet with id=AB6, first strand: chain 'C' and resid 290 through 294 removed outlier: 4.096A pdb=" N ASN C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 332 through 333 removed outlier: 3.930A pdb=" N SER C 310 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 332 through 333 removed outlier: 3.930A pdb=" N SER C 310 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 383 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 399 removed outlier: 3.590A pdb=" N ARG C 399 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 407 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 425 through 428 295 hydrogen bonds defined for protein. 744 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: 1.02 Time building geometry restraints manager: 0.58 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: 2349 1.34 - 1.46: 1813 1.46 - 1.58: 3316 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 7524 Sorted by residual: bond pdb=" N PCA B 26 " pdb=" CD PCA B 26 " ideal model delta sigma weight residual 1.345 1.464 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" N PCA C 26 " pdb=" CD PCA C 26 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" CG TRP B 474 " pdb=" CD1 TRP B 474 " ideal model delta sigma weight residual 1.365 1.477 -0.112 2.50e-02 1.60e+03 2.01e+01 bond pdb=" CG TRP B 272 " pdb=" CD1 TRP B 272 " ideal model delta sigma weight residual 1.365 1.476 -0.111 2.50e-02 1.60e+03 1.98e+01 bond pdb=" CG TRP C 272 " pdb=" CD1 TRP C 272 " ideal model delta sigma weight residual 1.365 1.476 -0.111 2.50e-02 1.60e+03 1.97e+01 ... (remaining 7519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 10078 2.25 - 4.50: 204 4.50 - 6.75: 6 6.75 - 9.00: 3 9.00 - 11.25: 2 Bond angle restraints: 10293 Sorted by residual: angle pdb=" CD2 TRP C 269 " pdb=" CE2 TRP C 269 " pdb=" CZ2 TRP C 269 " ideal model delta sigma weight residual 122.40 118.01 4.39 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CD2 TRP B 269 " pdb=" CE2 TRP B 269 " pdb=" CZ2 TRP B 269 " ideal model delta sigma weight residual 122.40 118.04 4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CD2 TRP C 272 " pdb=" CE2 TRP C 272 " pdb=" CZ2 TRP C 272 " ideal model delta sigma weight residual 122.40 118.12 4.28 1.00e+00 1.00e+00 1.84e+01 angle pdb=" CD2 TRP C 474 " pdb=" CE2 TRP C 474 " pdb=" CZ2 TRP C 474 " ideal model delta sigma weight residual 122.40 118.15 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O PCA C 26 " pdb=" C PCA C 26 " pdb=" N ASP C 27 " ideal model delta sigma weight residual 123.00 116.24 6.76 1.60e+00 3.91e-01 1.79e+01 ... (remaining 10288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 4044 14.86 - 29.72: 238 29.72 - 44.57: 80 44.57 - 59.43: 20 59.43 - 74.29: 3 Dihedral angle restraints: 4385 sinusoidal: 1672 harmonic: 2713 Sorted by residual: dihedral pdb=" CA PHE B 383 " pdb=" C PHE B 383 " pdb=" N TRP B 384 " pdb=" CA TRP B 384 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" SG CYS C 193 " pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" CA CYS C 323 " ideal model delta sinusoidal sigma weight residual 79.00 22.61 56.39 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" N CYS B 352 " pdb=" CA CYS B 352 " pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " ideal model delta sinusoidal sigma weight residual 60.00 116.92 -56.92 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 745 0.028 - 0.055: 277 0.055 - 0.083: 75 0.083 - 0.110: 63 0.110 - 0.138: 7 Chirality restraints: 1167 Sorted by residual: chirality pdb=" CA PRO C 70 " pdb=" N PRO C 70 " pdb=" C PRO C 70 " pdb=" CB PRO C 70 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE B 330 " pdb=" N ILE B 330 " pdb=" C ILE B 330 " pdb=" CB ILE B 330 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE C 139 " pdb=" N ILE C 139 " pdb=" C ILE C 139 " pdb=" CB ILE C 139 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1164 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PCA C 26 " 0.048 2.00e-02 2.50e+03 9.22e-02 8.50e+01 pdb=" C PCA C 26 " -0.159 2.00e-02 2.50e+03 pdb=" O PCA C 26 " 0.060 2.00e-02 2.50e+03 pdb=" N ASP C 27 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PCA B 26 " 0.037 2.00e-02 2.50e+03 7.26e-02 5.28e+01 pdb=" C PCA B 26 " -0.126 2.00e-02 2.50e+03 pdb=" O PCA B 26 " 0.047 2.00e-02 2.50e+03 pdb=" N ASP B 27 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 103 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 104 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.021 5.00e-02 4.00e+02 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1101 2.76 - 3.30: 6778 3.30 - 3.83: 11606 3.83 - 4.37: 12670 4.37 - 4.90: 22748 Nonbonded interactions: 54903 Sorted by model distance: nonbonded pdb=" ND1 HIS C 412 " pdb=" OH TYR C 423 " model vdw 2.229 3.120 nonbonded pdb=" O SER B 318 " pdb=" OG SER B 360 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU C 156 " pdb=" OH TYR C 167 " model vdw 2.275 3.040 nonbonded pdb=" NE2 GLN C 302 " pdb=" O SER C 350 " model vdw 2.280 3.120 nonbonded pdb=" O SER C 318 " pdb=" OG SER C 360 " model vdw 2.308 3.040 ... (remaining 54898 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 26 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 173 or (resid 174 through 175 a \ nd (name N or name CA or name C or name O or name CB )) or resid 176 or (resid 1 \ 77 through 178 and (name N or name CA or name C or name O or name CB )) or resid \ 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 246 or (resid 247 and (name N or name CA or name C or name O or \ name CB )) or resid 248 through 294 or (resid 295 and (name N or name CA or nam \ e C or name O or name CB )) or resid 296 through 325 or (resid 326 through 327 a \ nd (name N or name CA or name C or name O or name CB )) or resid 328 through 329 \ or (resid 330 and (name N or name CA or name C or name O or name CB )) or resid \ 331 through 400 or resid 405 through 428 or (resid 435 through 437 and (name N \ or name CA or name C or name O or name CB )) or resid 438 through 450 or (resid \ 456 through 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 1006)) selection = (chain 'C' and (resid 26 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 326 o \ r (resid 327 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 28 through 334 or (resid 335 and (name N or name CA or name C or name O or name \ CB )) or resid 336 through 337 or (resid 348 through 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 397 or (resid 398 through \ 405 and (name N or name CA or name C or name O or name CB )) or resid 406 throu \ gh 1006)) } 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: 2.140 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.005 0.119 7550 Z= 0.242 Angle : 0.666 11.245 10339 Z= 0.356 Chirality : 0.037 0.138 1167 Planarity : 0.005 0.092 1314 Dihedral : 11.136 74.289 2587 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 5.64 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 916 helix: 2.74 (0.55), residues: 105 sheet: 0.61 (0.28), residues: 364 loop : -0.59 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 464 TYR 0.006 0.001 TYR C 423 PHE 0.007 0.001 PHE A 162 TRP 0.008 0.001 TRP C 272 HIS 0.002 0.000 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 ( 7524) covalent geometry : angle 0.66109 / 0.36 (10293) SS BOND : bond 0.00177 / 0.11 ( 14) SS BOND : angle 0.66877 / 0.51 ( 28) hydrogen bonds : bond 0.23302 / 16.72 ( 273) hydrogen bonds : angle 9.07650 / 6.57 ( 744) Misc. bond : bond 0.01069 / 0.66 ( 6) link_NAG-ASN : bond 0.00106 / 0.06 ( 6) link_NAG-ASN : angle 1.95924 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8820 (p0) cc_final: 0.8501 (p0) REVERT: B 49 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 140 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8464 (mmtm) REVERT: B 315 PHE cc_start: 0.7963 (p90) cc_final: 0.7559 (p90) REVERT: B 424 GLN cc_start: 0.7737 (pt0) cc_final: 0.7440 (pt0) REVERT: C 421 THR cc_start: 0.8514 (m) cc_final: 0.8301 (p) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 0.0678 time to fit residues: 12.0521 Evaluate side-chains 95 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 GLN B 304 GLN C 64 GLN C 151 GLN C 302 GLN C 306 GLN C 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095946 restraints weight = 14488.200| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.70 r_work: 0.3110 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7550 Z= 0.145 Angle : 0.636 13.140 10339 Z= 0.306 Chirality : 0.039 0.146 1167 Planarity : 0.005 0.050 1314 Dihedral : 5.539 44.580 1018 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.62 % Allowed : 9.13 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 916 helix: 2.62 (0.54), residues: 105 sheet: 0.61 (0.26), residues: 386 loop : -0.49 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.001 TYR C 470 PHE 0.020 0.001 PHE C 354 TRP 0.018 0.001 TRP C 410 HIS 0.004 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7524) covalent geometry : angle 0.62691 / 0.30 (10293) SS BOND : bond 0.00346 / 0.25 ( 14) SS BOND : angle 1.12455 / 1.14 ( 28) hydrogen bonds : bond 0.04139 / 2.86 ( 273) hydrogen bonds : angle 6.50710 / 4.75 ( 744) Misc. bond : bond 0.00078 / 0.04 ( 6) link_NAG-ASN : bond 0.00186 / 0.12 ( 6) link_NAG-ASN : angle 2.35116 / 1.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8446 (t) REVERT: B 287 LEU cc_start: 0.7237 (pt) cc_final: 0.6859 (tt) REVERT: B 315 PHE cc_start: 0.8076 (p90) cc_final: 0.7847 (p90) REVERT: B 477 TRP cc_start: 0.7412 (m100) cc_final: 0.6741 (m100) REVERT: C 142 MET cc_start: 0.8466 (ptt) cc_final: 0.8133 (ptp) REVERT: C 251 SER cc_start: 0.8810 (m) cc_final: 0.8312 (p) REVERT: C 421 THR cc_start: 0.8328 (m) cc_final: 0.8109 (p) outliers start: 27 outliers final: 12 residues processed: 117 average time/residue: 0.0595 time to fit residues: 10.2556 Evaluate side-chains 100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.0030 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.9270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN C 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094833 restraints weight = 14389.349| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.61 r_work: 0.3093 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7550 Z= 0.172 Angle : 0.643 12.973 10339 Z= 0.307 Chirality : 0.039 0.198 1167 Planarity : 0.005 0.049 1314 Dihedral : 5.061 43.249 1013 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.49 % Allowed : 10.60 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.29), residues: 916 helix: 2.52 (0.53), residues: 105 sheet: 0.49 (0.26), residues: 388 loop : -0.51 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.011 0.001 TYR B 316 PHE 0.017 0.001 PHE C 354 TRP 0.012 0.001 TRP B 272 HIS 0.002 0.001 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 7524) covalent geometry : angle 0.63585 / 0.31 (10293) SS BOND : bond 0.00382 / 0.27 ( 14) SS BOND : angle 1.01077 / 0.87 ( 28) hydrogen bonds : bond 0.03681 / 2.54 ( 273) hydrogen bonds : angle 5.89925 / 4.31 ( 744) Misc. bond : bond 0.00079 / 0.05 ( 6) link_NAG-ASN : bond 0.00154 / 0.08 ( 6) link_NAG-ASN : angle 2.08442 / 1.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 49 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8542 (t) REVERT: B 287 LEU cc_start: 0.7147 (pt) cc_final: 0.6830 (tt) REVERT: B 302 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 315 PHE cc_start: 0.8168 (p90) cc_final: 0.7885 (p90) REVERT: B 477 TRP cc_start: 0.7386 (m100) cc_final: 0.6706 (m100) REVERT: C 302 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.6011 (tm-30) REVERT: C 304 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: C 470 TYR cc_start: 0.8128 (m-80) cc_final: 0.7814 (m-80) outliers start: 26 outliers final: 17 residues processed: 116 average time/residue: 0.0661 time to fit residues: 11.0863 Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095036 restraints weight = 14701.219| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.66 r_work: 0.3092 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.140 Angle : 0.626 12.419 10339 Z= 0.297 Chirality : 0.039 0.174 1167 Planarity : 0.004 0.051 1314 Dihedral : 5.017 40.984 1013 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.76 % Allowed : 12.48 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.29), residues: 916 helix: 2.56 (0.53), residues: 105 sheet: 0.52 (0.26), residues: 387 loop : -0.53 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.010 0.001 TYR C 423 PHE 0.019 0.001 PHE C 354 TRP 0.009 0.001 TRP C 477 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7524) covalent geometry : angle 0.61811 / 0.30 (10293) SS BOND : bond 0.00318 / 0.21 ( 14) SS BOND : angle 0.97174 / 0.76 ( 28) hydrogen bonds : bond 0.03245 / 2.26 ( 273) hydrogen bonds : angle 5.55557 / 4.07 ( 744) Misc. bond : bond 0.00061 / 0.04 ( 6) link_NAG-ASN : bond 0.00233 / 0.15 ( 6) link_NAG-ASN : angle 2.23337 / 1.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8568 (t) REVERT: B 140 LYS cc_start: 0.8826 (mmtm) cc_final: 0.8503 (mmtm) REVERT: B 287 LEU cc_start: 0.7112 (pt) cc_final: 0.6800 (tt) REVERT: B 302 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 315 PHE cc_start: 0.8129 (p90) cc_final: 0.7894 (p90) REVERT: B 477 TRP cc_start: 0.7312 (m100) cc_final: 0.6612 (m100) REVERT: C 279 ASP cc_start: 0.8645 (m-30) cc_final: 0.8366 (m-30) REVERT: C 302 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6054 (tm-30) REVERT: C 304 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8261 (pm20) outliers start: 28 outliers final: 20 residues processed: 118 average time/residue: 0.0683 time to fit residues: 11.5534 Evaluate side-chains 105 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 89 optimal weight: 0.0030 chunk 40 optimal weight: 0.0670 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.136813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095818 restraints weight = 14540.996| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.64 r_work: 0.3107 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7550 Z= 0.116 Angle : 0.622 12.528 10339 Z= 0.293 Chirality : 0.038 0.162 1167 Planarity : 0.004 0.050 1314 Dihedral : 4.909 40.830 1013 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.36 % Allowed : 13.29 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 916 helix: 2.69 (0.53), residues: 105 sheet: 0.61 (0.26), residues: 385 loop : -0.51 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.011 0.001 TYR C 423 PHE 0.017 0.001 PHE C 115 TRP 0.008 0.001 TRP C 477 HIS 0.002 0.000 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7524) covalent geometry : angle 0.61561 / 0.29 (10293) SS BOND : bond 0.00405 / 0.31 ( 14) SS BOND : angle 0.96750 / 0.78 ( 28) hydrogen bonds : bond 0.02983 / 2.08 ( 273) hydrogen bonds : angle 5.28619 / 3.89 ( 744) Misc. bond : bond 0.00042 / 0.02 ( 6) link_NAG-ASN : bond 0.00096 / 0.05 ( 6) link_NAG-ASN : angle 1.94229 / 1.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8542 (t) REVERT: B 140 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8528 (mmtm) REVERT: B 287 LEU cc_start: 0.7099 (pt) cc_final: 0.6782 (tt) REVERT: B 302 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 315 PHE cc_start: 0.8059 (p90) cc_final: 0.7796 (p90) REVERT: B 477 TRP cc_start: 0.7334 (m100) cc_final: 0.6613 (m100) REVERT: C 304 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8450 (pm20) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.0685 time to fit residues: 10.8466 Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 0.0030 chunk 49 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096233 restraints weight = 14522.095| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.63 r_work: 0.3108 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7550 Z= 0.120 Angle : 0.617 11.661 10339 Z= 0.290 Chirality : 0.038 0.150 1167 Planarity : 0.004 0.050 1314 Dihedral : 4.874 41.056 1013 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.76 % Allowed : 13.83 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.29), residues: 916 helix: 2.63 (0.53), residues: 105 sheet: 0.66 (0.26), residues: 385 loop : -0.49 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.012 0.001 TYR B 328 PHE 0.015 0.001 PHE C 115 TRP 0.008 0.001 TRP C 477 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 7524) covalent geometry : angle 0.61179 / 0.29 (10293) SS BOND : bond 0.00317 / 0.20 ( 14) SS BOND : angle 0.97915 / 0.81 ( 28) hydrogen bonds : bond 0.02948 / 2.06 ( 273) hydrogen bonds : angle 5.11796 / 3.77 ( 744) Misc. bond : bond 0.00044 / 0.03 ( 6) link_NAG-ASN : bond 0.00094 / 0.05 ( 6) link_NAG-ASN : angle 1.78063 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8579 (t) REVERT: B 140 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8557 (mmtm) REVERT: B 287 LEU cc_start: 0.7088 (pt) cc_final: 0.6771 (tt) REVERT: B 302 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 315 PHE cc_start: 0.8055 (p90) cc_final: 0.7805 (p90) REVERT: C 302 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: C 304 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (pm20) outliers start: 28 outliers final: 20 residues processed: 113 average time/residue: 0.0687 time to fit residues: 11.0088 Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096426 restraints weight = 14603.492| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.73 r_work: 0.3119 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7550 Z= 0.107 Angle : 0.623 13.597 10339 Z= 0.291 Chirality : 0.038 0.142 1167 Planarity : 0.004 0.050 1314 Dihedral : 4.782 40.654 1013 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.49 % Allowed : 15.03 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 916 helix: 2.55 (0.53), residues: 107 sheet: 0.80 (0.26), residues: 384 loop : -0.48 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.012 0.001 TYR B 328 PHE 0.015 0.001 PHE C 115 TRP 0.008 0.001 TRP C 477 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7524) covalent geometry : angle 0.61848 / 0.29 (10293) SS BOND : bond 0.00262 / 0.17 ( 14) SS BOND : angle 1.03397 / 1.12 ( 28) hydrogen bonds : bond 0.02788 / 1.95 ( 273) hydrogen bonds : angle 4.96656 / 3.67 ( 744) Misc. bond : bond 0.00033 / 0.02 ( 6) link_NAG-ASN : bond 0.00086 / 0.05 ( 6) link_NAG-ASN : angle 1.67233 / 1.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8522 (t) REVERT: B 140 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8604 (mmtm) REVERT: B 287 LEU cc_start: 0.7121 (pt) cc_final: 0.6801 (tt) REVERT: B 302 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 315 PHE cc_start: 0.8031 (p90) cc_final: 0.7766 (p90) REVERT: B 376 HIS cc_start: 0.8777 (m-70) cc_final: 0.8521 (m-70) REVERT: C 302 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5827 (tm-30) REVERT: C 304 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (pm20) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.0603 time to fit residues: 9.5504 Evaluate side-chains 112 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.134835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093230 restraints weight = 14571.980| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.64 r_work: 0.3066 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7550 Z= 0.240 Angle : 0.688 13.517 10339 Z= 0.327 Chirality : 0.040 0.167 1167 Planarity : 0.005 0.056 1314 Dihedral : 5.285 43.987 1013 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.49 % Allowed : 15.84 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.29), residues: 916 helix: 2.32 (0.53), residues: 105 sheet: 0.45 (0.27), residues: 376 loop : -0.42 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.012 0.001 TYR B 328 PHE 0.014 0.002 PHE C 105 TRP 0.012 0.001 TRP B 272 HIS 0.004 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 ( 7524) covalent geometry : angle 0.68131 / 0.32 (10293) SS BOND : bond 0.00420 / 0.34 ( 14) SS BOND : angle 1.32682 / 1.51 ( 28) hydrogen bonds : bond 0.03669 / 2.52 ( 273) hydrogen bonds : angle 5.25011 / 3.88 ( 744) Misc. bond : bond 0.00088 / 0.05 ( 6) link_NAG-ASN : bond 0.00187 / 0.11 ( 6) link_NAG-ASN : angle 1.95553 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8667 (t) REVERT: B 112 LYS cc_start: 0.7917 (tttp) cc_final: 0.7712 (tttp) REVERT: B 140 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8527 (mmtm) REVERT: B 287 LEU cc_start: 0.7087 (pt) cc_final: 0.6808 (tt) REVERT: C 56 GLU cc_start: 0.8431 (mp0) cc_final: 0.8084 (mp0) REVERT: C 279 ASP cc_start: 0.8755 (m-30) cc_final: 0.8511 (m-30) REVERT: C 302 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: C 304 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: C 464 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7162 (ttm-80) outliers start: 26 outliers final: 20 residues processed: 109 average time/residue: 0.0637 time to fit residues: 9.9906 Evaluate side-chains 102 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094225 restraints weight = 14662.416| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.74 r_work: 0.3075 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7550 Z= 0.141 Angle : 0.676 14.836 10339 Z= 0.316 Chirality : 0.039 0.148 1167 Planarity : 0.005 0.055 1314 Dihedral : 5.091 41.629 1013 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.95 % Allowed : 16.64 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.29), residues: 916 helix: 2.47 (0.53), residues: 105 sheet: 0.58 (0.26), residues: 381 loop : -0.48 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.014 0.001 TYR B 328 PHE 0.014 0.001 PHE C 115 TRP 0.014 0.001 TRP C 398 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 7524) covalent geometry : angle 0.67061 / 0.31 (10293) SS BOND : bond 0.00286 / 0.18 ( 14) SS BOND : angle 1.17967 / 1.26 ( 28) hydrogen bonds : bond 0.03133 / 2.18 ( 273) hydrogen bonds : angle 5.07133 / 3.76 ( 744) Misc. bond : bond 0.00045 / 0.03 ( 6) link_NAG-ASN : bond 0.00103 / 0.05 ( 6) link_NAG-ASN : angle 1.84292 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8564 (t) REVERT: B 140 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8590 (mmtm) REVERT: B 287 LEU cc_start: 0.7109 (pt) cc_final: 0.6812 (tt) REVERT: B 302 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 56 GLU cc_start: 0.8469 (mp0) cc_final: 0.8160 (mp0) REVERT: C 302 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: C 304 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8251 (pm20) outliers start: 22 outliers final: 18 residues processed: 103 average time/residue: 0.0695 time to fit residues: 10.2111 Evaluate side-chains 105 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094723 restraints weight = 14598.961| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.67 r_work: 0.3089 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.142 Angle : 0.656 14.455 10339 Z= 0.308 Chirality : 0.039 0.151 1167 Planarity : 0.005 0.056 1314 Dihedral : 5.080 41.159 1013 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.82 % Allowed : 16.51 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.29), residues: 916 helix: 2.46 (0.53), residues: 105 sheet: 0.61 (0.27), residues: 379 loop : -0.52 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.012 0.001 TYR B 328 PHE 0.025 0.002 PHE B 315 TRP 0.008 0.001 TRP B 272 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 7524) covalent geometry : angle 0.65001 / 0.31 (10293) SS BOND : bond 0.00407 / 0.27 ( 14) SS BOND : angle 1.22864 / 1.31 ( 28) hydrogen bonds : bond 0.03111 / 2.17 ( 273) hydrogen bonds : angle 4.96963 / 3.69 ( 744) Misc. bond : bond 0.00047 / 0.03 ( 6) link_NAG-ASN : bond 0.00093 / 0.05 ( 6) link_NAG-ASN : angle 1.80573 / 1.26 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8520 (mmtm) REVERT: B 287 LEU cc_start: 0.7068 (pt) cc_final: 0.6772 (tt) REVERT: B 302 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 477 TRP cc_start: 0.7341 (m100) cc_final: 0.6568 (m100) REVERT: C 56 GLU cc_start: 0.8414 (mp0) cc_final: 0.8083 (mp0) REVERT: C 302 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: C 304 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8244 (pm20) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.0672 time to fit residues: 9.6053 Evaluate side-chains 102 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 304 GLN Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.136761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095494 restraints weight = 14711.819| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.68 r_work: 0.3106 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7550 Z= 0.125 Angle : 0.649 13.996 10339 Z= 0.304 Chirality : 0.039 0.149 1167 Planarity : 0.004 0.055 1314 Dihedral : 4.935 41.473 1012 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.82 % Allowed : 16.64 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 916 helix: 2.53 (0.53), residues: 105 sheet: 0.69 (0.27), residues: 382 loop : -0.55 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.013 0.001 TYR C 423 PHE 0.016 0.001 PHE C 115 TRP 0.007 0.001 TRP B 272 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 ( 7524) covalent geometry : angle 0.64301 / 0.30 (10293) SS BOND : bond 0.00323 / 0.21 ( 14) SS BOND : angle 1.16901 / 1.27 ( 28) hydrogen bonds : bond 0.02941 / 2.04 ( 273) hydrogen bonds : angle 4.91272 / 3.66 ( 744) Misc. bond : bond 0.00037 / 0.02 ( 6) link_NAG-ASN : bond 0.00075 / 0.04 ( 6) link_NAG-ASN : angle 1.74683 / 1.21 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.74 seconds wall clock time: 30 minutes 7.68 seconds (1807.68 seconds total)