Starting phenix.real_space_refine on Fri Aug 22 20:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g04_29644/08_2025/8g04_29644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g04_29644/08_2025/8g04_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g04_29644/08_2025/8g04_29644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g04_29644/08_2025/8g04_29644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g04_29644/08_2025/8g04_29644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g04_29644/08_2025/8g04_29644.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 18 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.37, per 1000 atoms: 0.19 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: 0.60 Conformation dependent library (CDL) restraints added in 360.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 0.93 Time building geometry restraints manager: 0.81 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: 4250 14.86 - 29.72: 264 29.72 - 44.57: 84 44.57 - 59.43: 24 59.43 - 74.29: 3 Dihedral angle restraints: 4625 sinusoidal: 1912 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 4622 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.460 Find NCS groups from input model: 0.070 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 11.250 74.289 2827 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 aren 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 covalent geometry : bond 0.00514 ( 7524) covalent geometry : angle 0.66109 (10293) SS BOND : bond 0.00177 ( 14) SS BOND : angle 0.66877 ( 28) hydrogen bonds : bond 0.23302 ( 273) hydrogen bonds : angle 9.07650 ( 744) Misc. bond : bond 0.01069 ( 6) link_NAG-ASN : bond 0.00106 ( 6) link_NAG-ASN : angle 1.95924 ( 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 : 0.169 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: 0.8513 (m) cc_final: 0.8301 (p) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 0.0652 time to fit residues: 11.2801 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 : 0.161 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3919 r_free = 0.3919 target = 0.137373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096032 restraints weight = 14490.232| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.69 r_work: 0.3112 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1242 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 : 0.638 13.010 10339 Z= 0.307 Chirality : 0.039 0.146 1167 Planarity : 0.005 0.049 1314 Dihedral : 6.397 58.965 1258 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.49 % Allowed : 9.26 % 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 aren not related in a simple way. whole: 0.49 (0.29), residues: 916 helix: 2.61 (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 0.006 0.000 ARG C 319 TYR 0.017 0.001 TYR C 470 PHE 0.023 0.001 PHE C 354 TRP 0.019 0.001 TRP C 410 HIS 0.004 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7524) covalent geometry : angle 0.62812 (10293) SS BOND : bond 0.00432 ( 14) SS BOND : angle 1.15729 ( 28) hydrogen bonds : bond 0.04027 ( 273) hydrogen bonds : angle 6.52450 ( 744) Misc. bond : bond 0.00072 ( 6) link_NAG-ASN : bond 0.00181 ( 6) link_NAG-ASN : angle 2.43432 ( 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: 26 poor density : 94 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (t) REVERT: B 287 LEU cc_start: 0.7249 (pt) cc_final: 0.6872 (tt) REVERT: B 315 PHE cc_start: 0.8073 (p90) cc_final: 0.7843 (p90) REVERT: B 477 TRP cc_start: 0.7407 (m100) cc_final: 0.6768 (m100) REVERT: C 251 SER cc_start: 0.8811 (m) cc_final: 0.8314 (p) REVERT: C 421 THR cc_start: 0.8325 (m) cc_final: 0.8118 (p) outliers start: 26 outliers final: 12 residues processed: 117 average time/residue: 0.0734 time to fit residues: 12.4139 Evaluate side-chains 98 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.0060 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3901 r_free = 0.3901 target = 0.135847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094275 restraints weight = 14406.332| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.63 r_work: 0.3076 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7550 Z= 0.192 Angle : 0.655 13.018 10339 Z= 0.314 Chirality : 0.040 0.194 1167 Planarity : 0.005 0.051 1314 Dihedral : 5.801 53.012 1253 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.49 % Allowed : 10.74 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.29), residues: 916 helix: 2.47 (0.53), residues: 105 sheet: 0.50 (0.26), residues: 388 loop : -0.53 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 462 TYR 0.015 0.002 TYR B 328 PHE 0.017 0.002 PHE C 354 TRP 0.013 0.001 TRP B 272 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 7524) covalent geometry : angle 0.64697 (10293) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.03774 ( 28) hydrogen bonds : bond 0.03803 ( 273) hydrogen bonds : angle 5.95616 ( 744) Misc. bond : bond 0.00085 ( 6) link_NAG-ASN : bond 0.00149 ( 6) link_NAG-ASN : angle 2.28269 ( 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 116 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8560 (t) REVERT: B 287 LEU cc_start: 0.7170 (pt) cc_final: 0.6867 (tt) REVERT: B 302 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 315 PHE cc_start: 0.8197 (p90) cc_final: 0.7929 (p90) REVERT: B 477 TRP cc_start: 0.7399 (m100) cc_final: 0.6754 (m100) REVERT: C 304 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: C 470 TYR cc_start: 0.8176 (m-80) cc_final: 0.7856 (m-80) outliers start: 26 outliers final: 18 residues processed: 114 average time/residue: 0.0738 time to fit residues: 12.1287 Evaluate side-chains 103 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 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: 0.0000 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094960 restraints weight = 14784.264| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.78 r_work: 0.3091 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7550 Z= 0.122 Angle : 0.623 12.386 10339 Z= 0.294 Chirality : 0.039 0.175 1167 Planarity : 0.004 0.049 1314 Dihedral : 5.482 54.042 1253 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.62 % Allowed : 12.75 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.29), residues: 916 helix: 2.60 (0.53), residues: 105 sheet: 0.59 (0.26), residues: 384 loop : -0.55 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 462 TYR 0.014 0.001 TYR B 328 PHE 0.013 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 covalent geometry : bond 0.00293 ( 7524) covalent geometry : angle 0.61448 (10293) SS BOND : bond 0.00298 ( 14) SS BOND : angle 1.01293 ( 28) hydrogen bonds : bond 0.03132 ( 273) hydrogen bonds : angle 5.52111 ( 744) Misc. bond : bond 0.00046 ( 6) link_NAG-ASN : bond 0.00114 ( 6) link_NAG-ASN : angle 2.36343 ( 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 125 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8515 (t) REVERT: B 140 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8506 (mmtm) REVERT: B 287 LEU cc_start: 0.7155 (pt) cc_final: 0.6843 (tt) REVERT: B 302 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 315 PHE cc_start: 0.8111 (p90) cc_final: 0.7871 (p90) REVERT: B 477 TRP cc_start: 0.7309 (m100) cc_final: 0.6622 (m100) REVERT: C 99 GLU cc_start: 0.8765 (tt0) cc_final: 0.8550 (mt-10) REVERT: C 279 ASP cc_start: 0.8688 (m-30) cc_final: 0.8408 (m-30) REVERT: C 304 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8254 (pm20) outliers start: 27 outliers final: 18 residues processed: 121 average time/residue: 0.0796 time to fit residues: 13.7899 Evaluate side-chains 104 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 80 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.0010 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096838 restraints weight = 14504.077| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.71 r_work: 0.3123 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7550 Z= 0.100 Angle : 0.619 12.177 10339 Z= 0.290 Chirality : 0.038 0.164 1167 Planarity : 0.004 0.047 1314 Dihedral : 5.218 54.303 1253 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.49 % Allowed : 13.42 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.29), residues: 916 helix: 2.57 (0.54), residues: 107 sheet: 0.69 (0.26), residues: 387 loop : -0.48 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.013 0.001 TYR B 328 PHE 0.020 0.001 PHE C 354 TRP 0.008 0.001 TRP C 477 HIS 0.003 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7524) covalent geometry : angle 0.61254 (10293) SS BOND : bond 0.00278 ( 14) SS BOND : angle 0.95577 ( 28) hydrogen bonds : bond 0.02813 ( 273) hydrogen bonds : angle 5.14531 ( 744) Misc. bond : bond 0.00027 ( 6) link_NAG-ASN : bond 0.00138 ( 6) link_NAG-ASN : angle 1.96020 ( 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 118 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8475 (t) REVERT: B 140 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8528 (mmtm) REVERT: B 287 LEU cc_start: 0.7110 (pt) cc_final: 0.6799 (tt) REVERT: B 302 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 315 PHE cc_start: 0.8046 (p90) cc_final: 0.7746 (p90) REVERT: B 477 TRP cc_start: 0.7321 (m100) cc_final: 0.6598 (m100) REVERT: C 302 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5940 (tm-30) REVERT: C 304 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8440 (pm20) outliers start: 26 outliers final: 18 residues processed: 115 average time/residue: 0.0792 time to fit residues: 12.7969 Evaluate side-chains 106 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL 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 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 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: 0.0060 chunk 27 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.0070 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 overall best weight: 0.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.139721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098775 restraints weight = 14620.087| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.73 r_work: 0.3160 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7550 Z= 0.092 Angle : 0.614 11.450 10339 Z= 0.286 Chirality : 0.038 0.145 1167 Planarity : 0.004 0.047 1314 Dihedral : 4.926 54.649 1253 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.82 % Allowed : 14.50 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.29), residues: 916 helix: 2.54 (0.53), residues: 108 sheet: 0.91 (0.26), residues: 381 loop : -0.47 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.012 0.001 TYR B 328 PHE 0.016 0.001 PHE C 115 TRP 0.009 0.001 TRP B 110 HIS 0.001 0.000 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7524) covalent geometry : angle 0.60872 (10293) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.97248 ( 28) hydrogen bonds : bond 0.02606 ( 273) hydrogen bonds : angle 4.84691 ( 744) Misc. bond : bond 0.00012 ( 6) link_NAG-ASN : bond 0.00099 ( 6) link_NAG-ASN : angle 1.73950 ( 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 115 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 LEU cc_start: 0.7088 (pt) cc_final: 0.6762 (tt) REVERT: B 315 PHE cc_start: 0.7920 (p90) cc_final: 0.7640 (p90) REVERT: B 376 HIS cc_start: 0.8725 (m-70) cc_final: 0.8487 (m-70) REVERT: B 424 GLN cc_start: 0.7360 (pt0) cc_final: 0.6889 (pt0) REVERT: B 477 TRP cc_start: 0.7408 (m100) cc_final: 0.6253 (m100) REVERT: C 279 ASP cc_start: 0.8655 (m-30) cc_final: 0.8404 (m-30) REVERT: C 302 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5763 (tm-30) REVERT: C 304 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8184 (pm20) outliers start: 21 outliers final: 12 residues processed: 113 average time/residue: 0.0766 time to fit residues: 12.1841 Evaluate side-chains 99 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 185 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 HIS ** 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 = 0.3936 r_free = 0.3936 target = 0.138127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096842 restraints weight = 14638.847| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.72 r_work: 0.3126 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7550 Z= 0.121 Angle : 0.631 13.527 10339 Z= 0.294 Chirality : 0.039 0.156 1167 Planarity : 0.004 0.049 1314 Dihedral : 4.809 53.325 1250 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.95 % Allowed : 15.30 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.29), residues: 916 helix: 2.45 (0.53), residues: 108 sheet: 0.81 (0.26), residues: 385 loop : -0.43 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.018 0.001 TYR B 328 PHE 0.014 0.001 PHE C 354 TRP 0.007 0.001 TRP C 477 HIS 0.009 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7524) covalent geometry : angle 0.62446 (10293) SS BOND : bond 0.00292 ( 14) SS BOND : angle 1.20975 ( 28) hydrogen bonds : bond 0.02796 ( 273) hydrogen bonds : angle 4.85677 ( 744) Misc. bond : bond 0.00041 ( 6) link_NAG-ASN : bond 0.00075 ( 6) link_NAG-ASN : angle 1.78011 ( 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 108 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 LEU cc_start: 0.7116 (pt) cc_final: 0.6788 (tt) REVERT: B 315 PHE cc_start: 0.7950 (p90) cc_final: 0.7703 (p90) REVERT: B 376 HIS cc_start: 0.8751 (m-70) cc_final: 0.8506 (m-70) REVERT: B 477 TRP cc_start: 0.7448 (m100) cc_final: 0.6649 (m100) REVERT: C 56 GLU cc_start: 0.8458 (mp0) cc_final: 0.8170 (mp0) REVERT: C 302 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5823 (tm-30) REVERT: C 304 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8205 (pm20) outliers start: 22 outliers final: 17 residues processed: 105 average time/residue: 0.0800 time to fit residues: 11.9841 Evaluate side-chains 103 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 HIS ** 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 = 0.3921 r_free = 0.3921 target = 0.137055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095933 restraints weight = 14570.478| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.65 r_work: 0.3106 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7550 Z= 0.147 Angle : 0.652 14.005 10339 Z= 0.304 Chirality : 0.039 0.175 1167 Planarity : 0.004 0.051 1314 Dihedral : 4.896 52.803 1250 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.09 % Allowed : 16.38 % 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 aren not related in a simple way. whole: 0.62 (0.29), residues: 916 helix: 2.60 (0.53), residues: 105 sheet: 0.77 (0.26), residues: 388 loop : -0.47 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.016 0.001 TYR B 328 PHE 0.013 0.001 PHE C 354 TRP 0.008 0.001 TRP B 272 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7524) covalent geometry : angle 0.64575 (10293) SS BOND : bond 0.00317 ( 14) SS BOND : angle 1.22749 ( 28) hydrogen bonds : bond 0.03027 ( 273) hydrogen bonds : angle 4.91127 ( 744) Misc. bond : bond 0.00057 ( 6) link_NAG-ASN : bond 0.00092 ( 6) link_NAG-ASN : angle 1.82879 ( 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 109 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 LEU cc_start: 0.7049 (pt) cc_final: 0.6751 (tt) REVERT: B 315 PHE cc_start: 0.7987 (p90) cc_final: 0.7748 (p90) REVERT: B 376 HIS cc_start: 0.8751 (m-70) cc_final: 0.8493 (m-70) REVERT: C 56 GLU cc_start: 0.8412 (mp0) cc_final: 0.8130 (mp0) REVERT: C 279 ASP cc_start: 0.8700 (m-30) cc_final: 0.8467 (m-30) REVERT: C 302 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5889 (tm-30) REVERT: C 304 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: C 464 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7194 (ttm-80) outliers start: 23 outliers final: 18 residues processed: 106 average time/residue: 0.0725 time to fit residues: 11.0280 Evaluate side-chains 109 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.8445 > 50: distance: 17 - 39: 34.440 distance: 20 - 36: 17.832 distance: 31 - 36: 16.837 distance: 36 - 37: 13.632 distance: 37 - 38: 25.896 distance: 37 - 40: 11.662 distance: 38 - 39: 49.879 distance: 38 - 44: 18.348 distance: 40 - 41: 17.004 distance: 40 - 42: 20.554 distance: 41 - 43: 33.948 distance: 44 - 45: 16.371 distance: 45 - 48: 40.158 distance: 46 - 53: 14.303 distance: 48 - 49: 39.498 distance: 49 - 50: 27.604 distance: 50 - 51: 12.575 distance: 50 - 52: 10.598 distance: 53 - 54: 30.415 distance: 54 - 55: 11.568 distance: 54 - 57: 22.045 distance: 55 - 56: 6.532 distance: 55 - 61: 10.776 distance: 57 - 58: 35.972 distance: 58 - 60: 39.014 distance: 61 - 62: 23.623 distance: 62 - 63: 18.443 distance: 62 - 65: 43.544 distance: 63 - 64: 36.289 distance: 63 - 69: 4.232 distance: 69 - 70: 39.727 distance: 71 - 74: 40.492 distance: 74 - 75: 40.910 distance: 79 - 80: 39.453 distance: 81 - 82: 39.338 distance: 81 - 84: 36.416 distance: 84 - 85: 4.293 distance: 85 - 86: 24.221 distance: 86 - 87: 43.081 distance: 86 - 89: 25.606 distance: 91 - 95: 16.704 distance: 93 - 94: 55.923 distance: 94 - 138: 34.141 distance: 96 - 97: 39.124 distance: 96 - 99: 26.290 distance: 97 - 98: 31.099 distance: 97 - 101: 20.560 distance: 99 - 100: 44.012 distance: 100 - 118: 36.180