Starting phenix.real_space_refine on Wed Mar 12 07:57:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g04_29644/03_2025/8g04_29644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g04_29644/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g04_29644/03_2025/8g04_29644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g04_29644/03_2025/8g04_29644.map" model { file = "/net/cci-nas-00/data/ceres_data/8g04_29644/03_2025/8g04_29644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g04_29644/03_2025/8g04_29644.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 6, 'ASP:plan': 2, 'PCA:plan-2': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'PCA:plan-2': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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: 5.13, per 1000 atoms: 0.70 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: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.02 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: 2.14 Time building geometry restraints manager: 2.18 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 482 or resid 1001 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 482 or resid 1001 through 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: 1.850 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.110 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- 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 7524 Z= 0.334 Angle : 0.661 11.245 10293 Z= 0.355 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 272 HIS 0.002 0.000 HIS C 376 PHE 0.007 0.001 PHE A 162 TYR 0.006 0.001 TYR C 423 ARG 0.002 0.000 ARG C 464 *********************** 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 : 0.861 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: 0.1833 time to fit residues: 31.9185 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 : 0.735 ------------------------------------------------------------------------------- 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 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095587 restraints weight = 14358.737| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.67 r_work: 0.3094 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7524 Z= 0.245 Angle : 0.630 13.196 10293 Z= 0.305 Chirality : 0.039 0.145 1167 Planarity : 0.005 0.050 1314 Dihedral : 6.413 58.646 1258 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.36 % Allowed : 9.26 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 916 helix: 2.60 (0.54), residues: 105 sheet: 0.57 (0.26), residues: 386 loop : -0.49 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 410 HIS 0.003 0.001 HIS C 412 PHE 0.021 0.001 PHE C 354 TYR 0.017 0.001 TYR C 470 ARG 0.005 0.000 ARG C 319 *********************** 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 116 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 287 LEU cc_start: 0.7241 (pt) cc_final: 0.6864 (tt) REVERT: B 315 PHE cc_start: 0.8085 (p90) cc_final: 0.7853 (p90) REVERT: B 328 TYR cc_start: 0.7663 (m-10) cc_final: 0.7456 (m-10) REVERT: B 477 TRP cc_start: 0.7433 (m100) cc_final: 0.6799 (m100) outliers start: 25 outliers final: 13 residues processed: 113 average time/residue: 0.1569 time to fit residues: 25.5384 Evaluate side-chains 95 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 361 ILE 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 5 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.137093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095849 restraints weight = 14471.397| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.62 r_work: 0.3100 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7524 Z= 0.221 Angle : 0.619 12.940 10293 Z= 0.297 Chirality : 0.039 0.193 1167 Planarity : 0.005 0.048 1314 Dihedral : 5.654 53.990 1253 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.22 % Allowed : 11.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.29), residues: 916 helix: 2.63 (0.53), residues: 105 sheet: 0.54 (0.26), residues: 387 loop : -0.49 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 272 HIS 0.002 0.000 HIS C 376 PHE 0.016 0.001 PHE C 354 TYR 0.014 0.001 TYR B 316 ARG 0.002 0.000 ARG C 464 *********************** 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: 24 poor density : 92 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (t) REVERT: B 287 LEU cc_start: 0.7154 (pt) cc_final: 0.6832 (tt) REVERT: B 315 PHE cc_start: 0.8108 (p90) cc_final: 0.7825 (p90) REVERT: B 477 TRP cc_start: 0.7363 (m100) cc_final: 0.6688 (m100) REVERT: C 302 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6083 (tm-30) REVERT: C 304 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: C 470 TYR cc_start: 0.8163 (m-80) cc_final: 0.7840 (m-80) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 0.1664 time to fit residues: 26.7602 Evaluate side-chains 104 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL 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 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 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 464 ARG 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 19 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.135885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094343 restraints weight = 14684.407| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.74 r_work: 0.3077 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7524 Z= 0.258 Angle : 0.636 12.521 10293 Z= 0.303 Chirality : 0.041 0.430 1167 Planarity : 0.005 0.051 1314 Dihedral : 6.123 59.353 1253 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.03 % Allowed : 11.81 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.29), residues: 916 helix: 2.57 (0.53), residues: 105 sheet: 0.56 (0.26), residues: 386 loop : -0.53 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 272 HIS 0.004 0.001 HIS C 412 PHE 0.019 0.001 PHE C 354 TYR 0.015 0.001 TYR B 328 ARG 0.001 0.000 ARG C 426 *********************** 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 124 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.832 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: 0.8549 (t) REVERT: B 140 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8506 (mmtm) REVERT: B 287 LEU cc_start: 0.7166 (pt) cc_final: 0.6855 (tt) REVERT: B 315 PHE cc_start: 0.8139 (p90) cc_final: 0.7887 (p90) REVERT: B 477 TRP cc_start: 0.7329 (m100) cc_final: 0.6640 (m100) REVERT: C 279 ASP cc_start: 0.8736 (m-30) cc_final: 0.8479 (m-30) REVERT: C 304 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8290 (pm20) outliers start: 30 outliers final: 21 residues processed: 122 average time/residue: 0.1614 time to fit residues: 28.1719 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 : 0.820 ------------------------------------------------------------------------------- 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 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 352 CYS Chi-restraints excluded: chain C residue 361 ILE 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 15 optimal weight: 0.0570 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 overall best weight: 0.6116 ------------------------------------------------------------------------------- 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 = 0.136452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095210 restraints weight = 14390.097| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.70 r_work: 0.3096 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7524 Z= 0.211 Angle : 0.633 12.058 10293 Z= 0.300 Chirality : 0.043 0.606 1167 Planarity : 0.004 0.051 1314 Dihedral : 5.878 54.087 1253 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.49 % Allowed : 12.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 916 helix: 2.59 (0.53), residues: 105 sheet: 0.62 (0.26), residues: 382 loop : -0.52 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.003 0.001 HIS C 412 PHE 0.016 0.001 PHE C 354 TYR 0.015 0.001 TYR B 328 ARG 0.004 0.000 ARG C 319 *********************** 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 116 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (t) REVERT: B 140 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8505 (mmtm) REVERT: B 287 LEU cc_start: 0.7160 (pt) cc_final: 0.6856 (tt) REVERT: B 315 PHE cc_start: 0.8068 (p90) cc_final: 0.7800 (p90) REVERT: B 477 TRP cc_start: 0.7318 (m100) cc_final: 0.6617 (m100) REVERT: C 302 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5996 (tm-30) REVERT: C 304 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8256 (pm20) outliers start: 26 outliers final: 18 residues processed: 114 average time/residue: 0.1648 time to fit residues: 26.6614 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 : 0.882 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.132891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091338 restraints weight = 14579.577| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.63 r_work: 0.3028 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 7524 Z= 0.475 Angle : 0.717 11.949 10293 Z= 0.348 Chirality : 0.044 0.500 1167 Planarity : 0.005 0.057 1314 Dihedral : 6.311 50.466 1253 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.16 % Allowed : 13.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.28), residues: 916 helix: 1.79 (0.53), residues: 110 sheet: 0.24 (0.26), residues: 386 loop : -0.56 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 272 HIS 0.005 0.001 HIS A 142 PHE 0.016 0.002 PHE C 115 TYR 0.014 0.002 TYR B 328 ARG 0.003 0.000 ARG C 43 *********************** 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: 31 poor density : 84 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 140 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8541 (mmtm) REVERT: B 287 LEU cc_start: 0.7103 (pt) cc_final: 0.6852 (tt) REVERT: B 477 TRP cc_start: 0.7448 (m100) cc_final: 0.6750 (m100) REVERT: C 56 GLU cc_start: 0.8475 (mp0) cc_final: 0.8149 (mp0) REVERT: C 304 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: C 464 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6962 (ttp80) outliers start: 31 outliers final: 21 residues processed: 112 average time/residue: 0.1738 time to fit residues: 27.4365 Evaluate side-chains 103 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain C residue 150 LEU 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 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.0470 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.135526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094076 restraints weight = 14500.908| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.72 r_work: 0.3073 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7524 Z= 0.210 Angle : 0.648 12.985 10293 Z= 0.308 Chirality : 0.041 0.463 1167 Planarity : 0.005 0.054 1314 Dihedral : 5.788 53.760 1253 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.09 % Allowed : 15.30 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 916 helix: 2.52 (0.53), residues: 105 sheet: 0.42 (0.26), residues: 385 loop : -0.51 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 477 HIS 0.003 0.001 HIS C 412 PHE 0.017 0.001 PHE C 115 TYR 0.020 0.001 TYR C 423 ARG 0.007 0.000 ARG C 319 *********************** 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 109 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8573 (t) REVERT: B 140 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8542 (mmtm) REVERT: B 287 LEU cc_start: 0.7163 (pt) cc_final: 0.6857 (tt) REVERT: B 477 TRP cc_start: 0.7364 (m100) cc_final: 0.6696 (m100) REVERT: C 56 GLU cc_start: 0.8505 (mp0) cc_final: 0.8263 (mp0) REVERT: C 302 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: C 304 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: C 464 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6996 (ttp80) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.1798 time to fit residues: 26.3689 Evaluate side-chains 100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.134083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092687 restraints weight = 14601.716| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.62 r_work: 0.3052 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7524 Z= 0.339 Angle : 0.680 11.569 10293 Z= 0.324 Chirality : 0.043 0.440 1167 Planarity : 0.005 0.057 1314 Dihedral : 5.903 52.003 1253 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.09 % Allowed : 15.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 916 helix: 2.28 (0.53), residues: 105 sheet: 0.34 (0.26), residues: 383 loop : -0.56 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 272 HIS 0.004 0.001 HIS A 142 PHE 0.016 0.002 PHE C 115 TYR 0.016 0.001 TYR C 423 ARG 0.007 0.000 ARG C 319 *********************** 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 105 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 140 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8539 (mmtm) REVERT: B 287 LEU cc_start: 0.7104 (pt) cc_final: 0.6832 (tt) REVERT: B 328 TYR cc_start: 0.7663 (m-80) cc_final: 0.7372 (m-80) REVERT: B 477 TRP cc_start: 0.7370 (m100) cc_final: 0.6633 (m100) REVERT: C 56 GLU cc_start: 0.8471 (mp0) cc_final: 0.8223 (mp0) REVERT: C 302 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5935 (tm-30) REVERT: C 304 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: C 464 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6941 (ttp80) outliers start: 23 outliers final: 18 residues processed: 102 average time/residue: 0.1738 time to fit residues: 24.8869 Evaluate side-chains 100 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 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 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 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 0.0170 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.135928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094311 restraints weight = 14786.831| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.75 r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7524 Z= 0.220 Angle : 0.666 15.516 10293 Z= 0.312 Chirality : 0.041 0.426 1167 Planarity : 0.005 0.055 1314 Dihedral : 5.626 53.962 1253 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.68 % Allowed : 16.24 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.29), residues: 916 helix: 2.46 (0.53), residues: 105 sheet: 0.46 (0.26), residues: 386 loop : -0.62 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 110 HIS 0.003 0.001 HIS C 86 PHE 0.017 0.001 PHE C 115 TYR 0.018 0.001 TYR C 423 ARG 0.006 0.000 ARG C 319 *********************** 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 102 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (t) REVERT: B 140 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8551 (mmtm) REVERT: B 287 LEU cc_start: 0.7180 (pt) cc_final: 0.6856 (tt) REVERT: B 477 TRP cc_start: 0.7313 (m100) cc_final: 0.6587 (m100) REVERT: C 56 GLU cc_start: 0.8512 (mp0) cc_final: 0.8310 (mp0) REVERT: C 302 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.5887 (tm-30) REVERT: C 304 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8240 (pm20) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.1621 time to fit residues: 22.8232 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 : 0.755 ------------------------------------------------------------------------------- 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 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 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 361 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.137234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095655 restraints weight = 14626.497| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.75 r_work: 0.3103 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7524 Z= 0.175 Angle : 0.641 14.892 10293 Z= 0.301 Chirality : 0.041 0.417 1167 Planarity : 0.004 0.054 1314 Dihedral : 5.410 54.395 1253 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.42 % Allowed : 17.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 916 helix: 2.38 (0.54), residues: 107 sheet: 0.71 (0.27), residues: 374 loop : -0.47 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 110 HIS 0.003 0.000 HIS C 412 PHE 0.018 0.001 PHE C 115 TYR 0.019 0.001 TYR C 423 ARG 0.007 0.000 ARG C 319 ********************** 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 104 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8579 (mmtm) REVERT: B 287 LEU cc_start: 0.7135 (pt) cc_final: 0.6791 (tt) REVERT: B 477 TRP cc_start: 0.7304 (m100) cc_final: 0.6584 (m100) REVERT: C 56 GLU cc_start: 0.8354 (mp0) cc_final: 0.8148 (mp0) REVERT: C 302 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5939 (tm-30) REVERT: C 304 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8449 (pm20) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.1734 time to fit residues: 24.9232 Evaluate side-chains 104 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 47 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 57 optimal weight: 0.0020 overall best weight: 0.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.138199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096845 restraints weight = 14630.088| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.76 r_work: 0.3119 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7524 Z= 0.166 Angle : 0.643 14.521 10293 Z= 0.301 Chirality : 0.040 0.411 1167 Planarity : 0.004 0.051 1314 Dihedral : 5.249 54.675 1252 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.68 % Allowed : 17.18 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 916 helix: 2.43 (0.54), residues: 107 sheet: 0.81 (0.27), residues: 377 loop : -0.53 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 110 HIS 0.003 0.000 HIS C 412 PHE 0.018 0.001 PHE B 315 TYR 0.019 0.001 TYR C 423 ARG 0.006 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3915.03 seconds wall clock time: 67 minutes 53.92 seconds (4073.92 seconds total)