Starting phenix.real_space_refine on Sat Aug 23 22:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5a_42981/08_2025/8v5a_42981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5a_42981/08_2025/8v5a_42981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v5a_42981/08_2025/8v5a_42981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5a_42981/08_2025/8v5a_42981.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5a_42981/08_2025/8v5a_42981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5a_42981/08_2025/8v5a_42981.cif" } resolution = 3.0 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2628 atoms to isotropic. 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 54 5.16 5 C 8226 2.51 5 N 2232 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 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: 13056 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3476 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain breaks: 2 Chain: "Y" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Restraints were copied for chains: B, C, W, U Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13056 At special positions: 0 Unit cell: (125.55, 132.84, 132.84, 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 54 16.00 O 2544 8.00 N 2232 7.00 C 8226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.04 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.02 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.02 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 95 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 531.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 34.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 64 through 89 removed outlier: 4.545A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.712A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.568A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 190 removed outlier: 4.141A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 removed outlier: 4.445A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 487 Processing helix chain 'Y' and resid 86 through 90 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 64 through 89 removed outlier: 4.545A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix removed outlier: 3.712A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 139 through 152 removed outlier: 4.568A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.142A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 215 removed outlier: 4.445A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 487 Processing helix chain 'W' and resid 86 through 90 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 64 through 89 removed outlier: 4.545A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix removed outlier: 3.712A pdb=" N LEU C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.568A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 190 removed outlier: 4.141A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 215 removed outlier: 4.446A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 487 Processing helix chain 'U' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 30 through 52 current: chain 'A' and resid 169 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 173 current: chain 'A' and resid 263 through 270 removed outlier: 7.304A pdb=" N VAL A 264 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ARG A 281 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 326 current: chain 'A' and resid 337 through 339 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 337 through 339 current: chain 'Y' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 57 through 59 current: chain 'Y' and resid 103 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.986A pdb=" N GLY A 116 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 393 removed outlier: 7.232A pdb=" N LEU A 426 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE C 118 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 428 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 2 through 5 removed outlier: 3.537A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 52 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 52 current: chain 'B' and resid 169 through 173 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 173 current: chain 'B' and resid 263 through 270 removed outlier: 7.303A pdb=" N VAL B 264 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ARG B 281 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 322 through 326 current: chain 'B' and resid 337 through 339 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 337 through 339 current: chain 'W' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 57 through 59 current: chain 'W' and resid 103 through 106 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 93 removed outlier: 4.035A pdb=" N GLY B 116 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB2, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB3, first strand: chain 'W' and resid 2 through 5 removed outlier: 3.537A pdb=" N THR W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 30 through 52 current: chain 'C' and resid 169 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 173 current: chain 'C' and resid 263 through 270 removed outlier: 7.304A pdb=" N VAL C 264 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG C 281 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL C 266 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 326 current: chain 'C' and resid 337 through 339 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 337 through 339 current: chain 'U' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 57 through 59 current: chain 'U' and resid 103 through 106 Processing sheet with id=AB5, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB6, first strand: chain 'U' and resid 2 through 5 removed outlier: 3.537A pdb=" N THR U 77 " --> pdb=" O ASP U 72 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1425 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: 2.28 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3593 1.33 - 1.45: 2143 1.45 - 1.57: 7440 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 13248 Sorted by residual: bond pdb=" CG1 ILE B 262 " pdb=" CD1 ILE B 262 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.43e+00 bond pdb=" CG1 ILE C 262 " pdb=" CD1 ILE C 262 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.42e+00 bond pdb=" CG1 ILE A 262 " pdb=" CD1 ILE A 262 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CB ARG B 365 " pdb=" CG ARG B 365 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" CB ARG C 365 " pdb=" CG ARG C 365 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.32e+00 ... (remaining 13243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 16584 1.80 - 3.60: 1145 3.60 - 5.39: 199 5.39 - 7.19: 30 7.19 - 8.99: 9 Bond angle restraints: 17967 Sorted by residual: angle pdb=" N SER C 174 " pdb=" CA SER C 174 " pdb=" C SER C 174 " ideal model delta sigma weight residual 111.37 116.86 -5.49 1.64e+00 3.72e-01 1.12e+01 angle pdb=" N SER A 174 " pdb=" CA SER A 174 " pdb=" C SER A 174 " ideal model delta sigma weight residual 111.37 116.84 -5.47 1.64e+00 3.72e-01 1.11e+01 angle pdb=" N SER B 174 " pdb=" CA SER B 174 " pdb=" C SER B 174 " ideal model delta sigma weight residual 111.37 116.81 -5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" CA PRO B 81 " pdb=" N PRO B 81 " pdb=" CD PRO B 81 " ideal model delta sigma weight residual 112.00 107.39 4.61 1.40e+00 5.10e-01 1.09e+01 angle pdb=" CA TYR W 59 " pdb=" CB TYR W 59 " pdb=" CG TYR W 59 " ideal model delta sigma weight residual 113.90 119.81 -5.91 1.80e+00 3.09e-01 1.08e+01 ... (remaining 17962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7506 17.54 - 35.08: 483 35.08 - 52.62: 90 52.62 - 70.16: 15 70.16 - 87.70: 18 Dihedral angle restraints: 8112 sinusoidal: 3225 harmonic: 4887 Sorted by residual: dihedral pdb=" CA LYS A 173 " pdb=" C LYS A 173 " pdb=" N SER A 174 " pdb=" CA SER A 174 " ideal model delta harmonic sigma weight residual 180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LYS C 173 " pdb=" C LYS C 173 " pdb=" N SER C 174 " pdb=" CA SER C 174 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS B 173 " pdb=" C LYS B 173 " pdb=" N SER B 174 " pdb=" CA SER B 174 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 8109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1538 0.066 - 0.132: 541 0.132 - 0.198: 43 0.198 - 0.264: 5 0.264 - 0.330: 9 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CG LEU U 4 " pdb=" CB LEU U 4 " pdb=" CD1 LEU U 4 " pdb=" CD2 LEU U 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU W 4 " pdb=" CB LEU W 4 " pdb=" CD1 LEU W 4 " pdb=" CD2 LEU W 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU Y 4 " pdb=" CB LEU Y 4 " pdb=" CD1 LEU Y 4 " pdb=" CD2 LEU Y 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2133 not shown) Planarity restraints: 2307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 80 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 81 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 80 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO C 81 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 80 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO A 81 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.060 5.00e-02 4.00e+02 ... (remaining 2304 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 219 2.66 - 3.22: 12827 3.22 - 3.78: 20017 3.78 - 4.34: 28149 4.34 - 4.90: 46614 Nonbonded interactions: 107826 Sorted by model distance: nonbonded pdb=" NE2 GLN A 139 " pdb=" O GLU Y 1 " model vdw 2.106 3.120 nonbonded pdb=" OE1 GLU C 136 " pdb=" OG SER U 99 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLU A 136 " pdb=" OG SER Y 99 " model vdw 2.242 3.040 nonbonded pdb=" NE2 GLN C 139 " pdb=" O GLU U 1 " model vdw 2.247 3.120 nonbonded pdb=" NE2 GLN B 139 " pdb=" O GLU W 1 " model vdw 2.261 3.120 ... (remaining 107821 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'Y' selection = chain 'W' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 12.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 : 0.009 0.082 13266 Z= 0.338 Angle : 1.047 8.992 18003 Z= 0.580 Chirality : 0.064 0.330 2136 Planarity : 0.007 0.110 2307 Dihedral : 13.034 87.697 4920 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.64 (0.20), residues: 1677 helix: -0.35 (0.22), residues: 492 sheet: -0.23 (0.25), residues: 393 loop : -0.42 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG A 77 TYR 0.042 0.006 TYR A 438 PHE 0.024 0.004 PHE W 67 TRP 0.032 0.005 TRP C 308 HIS 0.015 0.005 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00855 (13248) covalent geometry : angle 1.04535 (17967) SS BOND : bond 0.00447 ( 18) SS BOND : angle 1.61679 ( 36) hydrogen bonds : bond 0.16649 ( 523) hydrogen bonds : angle 7.62169 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 362 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7382 (mm110) REVERT: A 413 THR cc_start: 0.7865 (p) cc_final: 0.7643 (m) REVERT: Y 31 ILE cc_start: 0.8385 (mm) cc_final: 0.8166 (mp) REVERT: B 84 ASP cc_start: 0.6974 (m-30) cc_final: 0.6669 (m-30) REVERT: W 99 SER cc_start: 0.7601 (t) cc_final: 0.7085 (t) REVERT: C 148 LYS cc_start: 0.7388 (mttt) cc_final: 0.7174 (mmmm) REVERT: C 362 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7369 (mm-40) REVERT: C 413 THR cc_start: 0.7945 (p) cc_final: 0.7653 (m) outliers start: 0 outliers final: 5 residues processed: 338 average time/residue: 0.6100 time to fit residues: 223.2259 Evaluate side-chains 325 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 320 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 399 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 229 GLN B 292 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN B 407 GLN ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN U 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121453 restraints weight = 18205.704| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.08 r_work: 0.3414 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13266 Z= 0.165 Angle : 0.656 7.602 18003 Z= 0.346 Chirality : 0.046 0.152 2136 Planarity : 0.005 0.072 2307 Dihedral : 5.479 29.114 1834 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.25 % Allowed : 9.68 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.21), residues: 1677 helix: 0.55 (0.23), residues: 495 sheet: -0.42 (0.24), residues: 411 loop : 0.08 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 81 TYR 0.021 0.002 TYR C 48 PHE 0.015 0.002 PHE U 67 TRP 0.010 0.002 TRP A 308 HIS 0.005 0.002 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00394 (13248) covalent geometry : angle 0.65608 (17967) SS BOND : bond 0.00170 ( 18) SS BOND : angle 0.59806 ( 36) hydrogen bonds : bond 0.04705 ( 523) hydrogen bonds : angle 5.66627 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 337 time to evaluate : 0.554 Fit side-chains REVERT: A 73 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7708 (ttt-90) REVERT: A 90 LYS cc_start: 0.6583 (mppt) cc_final: 0.6133 (mppt) REVERT: A 362 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 422 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7982 (mt) REVERT: A 472 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7299 (mm-30) REVERT: Y 31 ILE cc_start: 0.8476 (mm) cc_final: 0.8253 (mp) REVERT: B 73 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7908 (ttt180) REVERT: B 87 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7368 (ttm110) REVERT: B 319 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7958 (ttpt) REVERT: B 323 LEU cc_start: 0.8253 (tp) cc_final: 0.7783 (tt) REVERT: B 353 GLU cc_start: 0.7089 (tp30) cc_final: 0.6601 (tp30) REVERT: B 422 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8039 (mt) REVERT: W 29 SER cc_start: 0.8409 (p) cc_final: 0.8163 (m) REVERT: C 24 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8172 (mtpt) REVERT: C 413 THR cc_start: 0.8634 (p) cc_final: 0.8333 (m) REVERT: C 422 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7889 (mt) REVERT: C 464 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8127 (mtmp) outliers start: 33 outliers final: 15 residues processed: 343 average time/residue: 0.6334 time to fit residues: 234.4793 Evaluate side-chains 329 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 311 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 27 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 359 ASN A 399 ASN Y 103 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 272 ASN B 292 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 359 ASN C 395 ASN C 399 ASN U 103 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119641 restraints weight = 18396.234| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.12 r_work: 0.3378 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13266 Z= 0.225 Angle : 0.646 7.341 18003 Z= 0.337 Chirality : 0.047 0.152 2136 Planarity : 0.004 0.066 2307 Dihedral : 5.237 23.718 1826 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.27 % Allowed : 12.00 % Favored : 84.73 % 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: -0.02 (0.21), residues: 1677 helix: 0.75 (0.23), residues: 501 sheet: -0.75 (0.23), residues: 441 loop : 0.13 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 66 TYR 0.021 0.003 TYR B 48 PHE 0.016 0.002 PHE C 427 TRP 0.012 0.001 TRP W 106 HIS 0.006 0.002 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00547 (13248) covalent geometry : angle 0.64572 (17967) SS BOND : bond 0.00318 ( 18) SS BOND : angle 0.63416 ( 36) hydrogen bonds : bond 0.04358 ( 523) hydrogen bonds : angle 5.37516 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 0.504 Fit side-chains REVERT: A 22 ILE cc_start: 0.8215 (mt) cc_final: 0.7950 (mm) REVERT: A 23 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8249 (m) REVERT: A 148 LYS cc_start: 0.8196 (mttt) cc_final: 0.7909 (mtpt) REVERT: A 362 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8048 (mm110) REVERT: A 402 ASN cc_start: 0.7484 (m-40) cc_final: 0.7181 (m-40) REVERT: A 422 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 472 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7314 (mm-30) REVERT: Y 31 ILE cc_start: 0.8536 (mm) cc_final: 0.8334 (mp) REVERT: B 23 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 73 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7970 (ttt180) REVERT: B 207 TYR cc_start: 0.8285 (t80) cc_final: 0.8058 (t80) REVERT: B 319 LYS cc_start: 0.8270 (mtpp) cc_final: 0.8019 (ttpp) REVERT: B 323 LEU cc_start: 0.8248 (tp) cc_final: 0.7728 (tt) REVERT: B 353 GLU cc_start: 0.7234 (tp30) cc_final: 0.6651 (tp30) REVERT: B 420 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8020 (pp) REVERT: B 422 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8145 (mt) REVERT: W 29 SER cc_start: 0.8467 (p) cc_final: 0.8239 (m) REVERT: C 24 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8113 (mtmt) REVERT: C 413 THR cc_start: 0.8591 (p) cc_final: 0.8356 (m) REVERT: C 422 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7953 (mt) REVERT: C 462 LYS cc_start: 0.8121 (tppp) cc_final: 0.7894 (tppp) REVERT: U 29 SER cc_start: 0.8504 (p) cc_final: 0.8186 (m) outliers start: 48 outliers final: 17 residues processed: 348 average time/residue: 0.6414 time to fit residues: 241.1060 Evaluate side-chains 352 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 329 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 36 optimal weight: 0.0020 chunk 104 optimal weight: 0.8980 chunk 134 optimal weight: 0.4980 chunk 91 optimal weight: 0.0870 chunk 162 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 chunk 119 optimal weight: 0.0870 overall best weight: 0.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 350 HIS A 399 ASN A 407 GLN B 162 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN W 111 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 292 GLN C 359 ASN C 399 ASN U 103 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122982 restraints weight = 18350.581| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.14 r_work: 0.3424 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.043 13266 Z= 0.100 Angle : 0.553 8.040 18003 Z= 0.285 Chirality : 0.043 0.131 2136 Planarity : 0.004 0.054 2307 Dihedral : 4.810 20.327 1826 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 15.06 % Favored : 82.21 % 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: 0.07 (0.21), residues: 1677 helix: 1.04 (0.23), residues: 501 sheet: -1.01 (0.22), residues: 474 loop : 0.33 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 87 TYR 0.021 0.002 TYR A 207 PHE 0.008 0.001 PHE Y 67 TRP 0.009 0.001 TRP B 308 HIS 0.005 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00227 (13248) covalent geometry : angle 0.55336 (17967) SS BOND : bond 0.00107 ( 18) SS BOND : angle 0.60803 ( 36) hydrogen bonds : bond 0.03588 ( 523) hydrogen bonds : angle 5.05652 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 341 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8149 (m) REVERT: A 73 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7810 (ttt-90) REVERT: A 84 ASP cc_start: 0.8228 (m-30) cc_final: 0.7915 (m-30) REVERT: A 148 LYS cc_start: 0.8173 (mttt) cc_final: 0.7818 (mttt) REVERT: A 270 ASP cc_start: 0.7651 (t0) cc_final: 0.7426 (m-30) REVERT: A 362 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7985 (mm110) REVERT: A 409 VAL cc_start: 0.8800 (m) cc_final: 0.8544 (t) REVERT: A 422 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 472 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 23 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8218 (m) REVERT: B 73 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.7891 (ttt180) REVERT: B 84 ASP cc_start: 0.8033 (m-30) cc_final: 0.7748 (m-30) REVERT: B 281 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7998 (mtp85) REVERT: B 319 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7941 (ttpt) REVERT: B 323 LEU cc_start: 0.8208 (tp) cc_final: 0.7769 (tt) REVERT: B 353 GLU cc_start: 0.7227 (tp30) cc_final: 0.6651 (tp30) REVERT: B 422 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8110 (mt) REVERT: C 227 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8164 (mtpp) REVERT: C 413 THR cc_start: 0.8720 (p) cc_final: 0.8324 (m) REVERT: C 422 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7884 (mt) REVERT: C 462 LYS cc_start: 0.8113 (tppp) cc_final: 0.7867 (tppp) REVERT: U 27 SER cc_start: 0.8174 (t) cc_final: 0.7946 (p) REVERT: U 29 SER cc_start: 0.8445 (p) cc_final: 0.8075 (m) outliers start: 40 outliers final: 10 residues processed: 349 average time/residue: 0.5924 time to fit residues: 222.9840 Evaluate side-chains 340 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 324 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 107 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: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 395 ASN A 418 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN B 407 GLN C 127 GLN C 162 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120644 restraints weight = 18446.949| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.14 r_work: 0.3388 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13266 Z= 0.178 Angle : 0.590 6.915 18003 Z= 0.304 Chirality : 0.045 0.160 2136 Planarity : 0.004 0.056 2307 Dihedral : 4.883 24.860 1824 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.54 % Allowed : 15.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.21), residues: 1677 helix: 1.08 (0.23), residues: 501 sheet: -1.09 (0.22), residues: 474 loop : 0.27 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 375 TYR 0.021 0.002 TYR C 207 PHE 0.012 0.002 PHE C 427 TRP 0.008 0.001 TRP W 106 HIS 0.009 0.002 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00436 (13248) covalent geometry : angle 0.58824 (17967) SS BOND : bond 0.00201 ( 18) SS BOND : angle 1.08264 ( 36) hydrogen bonds : bond 0.03776 ( 523) hydrogen bonds : angle 5.03371 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 23 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 73 ARG cc_start: 0.8103 (ttt-90) cc_final: 0.7840 (ttt-90) REVERT: A 148 LYS cc_start: 0.8192 (mttt) cc_final: 0.7746 (mtpt) REVERT: A 362 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8051 (mm110) REVERT: A 422 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 23 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8238 (m) REVERT: B 84 ASP cc_start: 0.7975 (m-30) cc_final: 0.7735 (m-30) REVERT: B 281 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8004 (mtp85) REVERT: B 323 LEU cc_start: 0.8237 (tp) cc_final: 0.7826 (tt) REVERT: B 353 GLU cc_start: 0.7296 (tp30) cc_final: 0.6722 (tp30) REVERT: B 359 ASN cc_start: 0.8536 (t0) cc_final: 0.8072 (t0) REVERT: W 105 TYR cc_start: 0.8520 (m-80) cc_final: 0.8146 (m-80) REVERT: C 69 LYS cc_start: 0.7764 (tptp) cc_final: 0.7406 (ttmm) REVERT: C 227 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8205 (mtpp) REVERT: C 319 LYS cc_start: 0.8342 (mtpm) cc_final: 0.8031 (mtmm) REVERT: C 357 SER cc_start: 0.8121 (p) cc_final: 0.7904 (p) REVERT: C 413 THR cc_start: 0.8684 (p) cc_final: 0.8375 (m) REVERT: C 422 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7935 (mt) REVERT: C 462 LYS cc_start: 0.8099 (tppp) cc_final: 0.7813 (tppp) REVERT: U 29 SER cc_start: 0.8497 (p) cc_final: 0.8204 (m) outliers start: 52 outliers final: 23 residues processed: 338 average time/residue: 0.6193 time to fit residues: 227.1577 Evaluate side-chains 353 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120538 restraints weight = 18119.201| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.12 r_work: 0.3378 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13266 Z= 0.188 Angle : 0.585 6.767 18003 Z= 0.301 Chirality : 0.045 0.153 2136 Planarity : 0.004 0.055 2307 Dihedral : 4.882 22.510 1824 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.14 % Allowed : 16.77 % Favored : 80.10 % 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: -0.06 (0.21), residues: 1677 helix: 1.04 (0.23), residues: 504 sheet: -1.17 (0.22), residues: 474 loop : 0.21 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 375 TYR 0.025 0.002 TYR C 207 PHE 0.013 0.002 PHE C 427 TRP 0.007 0.001 TRP W 106 HIS 0.010 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00460 (13248) covalent geometry : angle 0.58313 (17967) SS BOND : bond 0.00170 ( 18) SS BOND : angle 1.08976 ( 36) hydrogen bonds : bond 0.03788 ( 523) hydrogen bonds : angle 5.00598 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 330 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8211 (mt) cc_final: 0.7871 (mm) REVERT: A 23 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8225 (m) REVERT: A 73 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7828 (ttt-90) REVERT: A 84 ASP cc_start: 0.8226 (m-30) cc_final: 0.7852 (m-30) REVERT: A 148 LYS cc_start: 0.8136 (mttt) cc_final: 0.7721 (mtpt) REVERT: A 357 SER cc_start: 0.8143 (p) cc_final: 0.7880 (p) REVERT: A 362 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8091 (mm110) REVERT: A 402 ASN cc_start: 0.7546 (m-40) cc_final: 0.7276 (m-40) REVERT: A 422 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 23 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8219 (m) REVERT: B 73 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7877 (ttt180) REVERT: B 84 ASP cc_start: 0.7994 (m-30) cc_final: 0.7772 (m-30) REVERT: B 281 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7954 (mtp85) REVERT: B 323 LEU cc_start: 0.8247 (tp) cc_final: 0.7839 (tt) REVERT: B 353 GLU cc_start: 0.7389 (tp30) cc_final: 0.6819 (tp30) REVERT: W 105 TYR cc_start: 0.8553 (m-80) cc_final: 0.8099 (m-80) REVERT: C 227 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8191 (mtpp) REVERT: C 255 ASP cc_start: 0.8170 (m-30) cc_final: 0.7954 (m-30) REVERT: C 357 SER cc_start: 0.8128 (p) cc_final: 0.7890 (p) REVERT: C 413 THR cc_start: 0.8672 (p) cc_final: 0.8351 (m) REVERT: C 422 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7941 (mt) REVERT: C 462 LYS cc_start: 0.8093 (tppp) cc_final: 0.7800 (tppp) REVERT: U 29 SER cc_start: 0.8495 (p) cc_final: 0.8228 (m) outliers start: 46 outliers final: 22 residues processed: 343 average time/residue: 0.6292 time to fit residues: 233.2638 Evaluate side-chains 348 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 72 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 18 optimal weight: 0.0070 chunk 142 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 152 optimal weight: 0.0020 chunk 128 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN A 461 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 399 ASN U 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.144773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122036 restraints weight = 18400.280| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.14 r_work: 0.3402 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13266 Z= 0.123 Angle : 0.547 7.303 18003 Z= 0.282 Chirality : 0.043 0.134 2136 Planarity : 0.004 0.050 2307 Dihedral : 4.702 21.326 1824 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.86 % Allowed : 18.20 % Favored : 78.94 % 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: -0.00 (0.21), residues: 1677 helix: 1.16 (0.23), residues: 504 sheet: -1.24 (0.22), residues: 474 loop : 0.28 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 375 TYR 0.025 0.002 TYR C 207 PHE 0.007 0.001 PHE C 427 TRP 0.006 0.001 TRP B 308 HIS 0.008 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00300 (13248) covalent geometry : angle 0.54688 (17967) SS BOND : bond 0.00109 ( 18) SS BOND : angle 0.74413 ( 36) hydrogen bonds : bond 0.03535 ( 523) hydrogen bonds : angle 4.89981 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.523 Fit side-chains REVERT: A 22 ILE cc_start: 0.8129 (mt) cc_final: 0.7808 (mm) REVERT: A 23 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8168 (m) REVERT: A 73 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.7855 (ttt-90) REVERT: A 84 ASP cc_start: 0.8196 (m-30) cc_final: 0.7874 (m-30) REVERT: A 148 LYS cc_start: 0.7983 (mttt) cc_final: 0.7605 (mtpt) REVERT: A 161 VAL cc_start: 0.5889 (OUTLIER) cc_final: 0.5660 (m) REVERT: A 362 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8002 (mm110) REVERT: A 402 ASN cc_start: 0.7531 (m-40) cc_final: 0.7218 (m-40) REVERT: A 422 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8128 (mt) REVERT: B 73 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.7874 (ttt180) REVERT: B 84 ASP cc_start: 0.7985 (m-30) cc_final: 0.7761 (m-30) REVERT: B 231 ILE cc_start: 0.8345 (mt) cc_final: 0.8065 (mp) REVERT: B 281 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7888 (mtp85) REVERT: B 323 LEU cc_start: 0.8224 (tp) cc_final: 0.7817 (tt) REVERT: B 353 GLU cc_start: 0.7398 (tp30) cc_final: 0.6824 (tp30) REVERT: W 105 TYR cc_start: 0.8552 (m-80) cc_final: 0.8139 (m-80) REVERT: C 22 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7836 (mm) REVERT: C 227 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8197 (mtpp) REVERT: C 255 ASP cc_start: 0.8175 (m-30) cc_final: 0.7951 (m-30) REVERT: C 279 GLN cc_start: 0.8614 (tt0) cc_final: 0.8380 (tt0) REVERT: C 357 SER cc_start: 0.8136 (p) cc_final: 0.7921 (p) REVERT: C 422 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 462 LYS cc_start: 0.8095 (tppp) cc_final: 0.7805 (tppp) REVERT: U 27 SER cc_start: 0.8247 (t) cc_final: 0.7904 (p) REVERT: U 29 SER cc_start: 0.8493 (p) cc_final: 0.8186 (m) outliers start: 42 outliers final: 20 residues processed: 335 average time/residue: 0.6689 time to fit residues: 241.8493 Evaluate side-chains 335 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 0.0370 chunk 142 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN A 407 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN B 407 GLN B 418 ASN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122764 restraints weight = 18248.611| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.12 r_work: 0.3413 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13266 Z= 0.120 Angle : 0.543 8.845 18003 Z= 0.277 Chirality : 0.043 0.169 2136 Planarity : 0.003 0.049 2307 Dihedral : 4.592 20.952 1824 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.52 % Allowed : 19.02 % Favored : 78.46 % 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: 0.07 (0.21), residues: 1677 helix: 1.26 (0.23), residues: 504 sheet: -1.22 (0.22), residues: 474 loop : 0.31 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 66 TYR 0.028 0.002 TYR C 207 PHE 0.007 0.001 PHE C 427 TRP 0.009 0.001 TRP B 308 HIS 0.009 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00290 (13248) covalent geometry : angle 0.54291 (17967) SS BOND : bond 0.00106 ( 18) SS BOND : angle 0.67653 ( 36) hydrogen bonds : bond 0.03467 ( 523) hydrogen bonds : angle 4.84221 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 322 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8101 (mt) cc_final: 0.7800 (mm) REVERT: A 73 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7799 (ttt-90) REVERT: A 84 ASP cc_start: 0.8184 (m-30) cc_final: 0.7866 (m-30) REVERT: A 148 LYS cc_start: 0.7978 (mttt) cc_final: 0.7587 (mtpt) REVERT: A 161 VAL cc_start: 0.4980 (OUTLIER) cc_final: 0.4775 (m) REVERT: A 307 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 402 ASN cc_start: 0.7486 (m-40) cc_final: 0.7139 (m-40) REVERT: A 422 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 73 ARG cc_start: 0.8088 (ttt-90) cc_final: 0.7839 (ttt180) REVERT: B 84 ASP cc_start: 0.7992 (m-30) cc_final: 0.7764 (m-30) REVERT: B 231 ILE cc_start: 0.8315 (mt) cc_final: 0.7991 (mp) REVERT: B 281 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7960 (mtp85) REVERT: B 323 LEU cc_start: 0.8206 (tp) cc_final: 0.7824 (tt) REVERT: B 353 GLU cc_start: 0.7407 (tp30) cc_final: 0.6866 (tp30) REVERT: B 359 ASN cc_start: 0.8460 (t0) cc_final: 0.8070 (t0) REVERT: W 105 TYR cc_start: 0.8558 (m-80) cc_final: 0.8238 (m-80) REVERT: C 22 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7818 (mm) REVERT: C 227 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8193 (mtpp) REVERT: C 255 ASP cc_start: 0.8141 (m-30) cc_final: 0.7909 (m-30) REVERT: C 357 SER cc_start: 0.8114 (p) cc_final: 0.7899 (p) REVERT: C 422 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7896 (mt) REVERT: C 462 LYS cc_start: 0.8064 (tppp) cc_final: 0.7772 (tppp) REVERT: U 27 SER cc_start: 0.8254 (t) cc_final: 0.7920 (p) REVERT: U 29 SER cc_start: 0.8474 (p) cc_final: 0.8168 (m) outliers start: 37 outliers final: 22 residues processed: 336 average time/residue: 0.6743 time to fit residues: 244.7151 Evaluate side-chains 339 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 159 optimal weight: 0.0370 chunk 151 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 113 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN A 362 GLN A 407 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN B 407 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 399 ASN U 103 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123468 restraints weight = 18547.088| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.16 r_work: 0.3423 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13266 Z= 0.111 Angle : 0.544 9.011 18003 Z= 0.276 Chirality : 0.043 0.152 2136 Planarity : 0.003 0.048 2307 Dihedral : 4.510 19.971 1824 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.32 % Allowed : 19.43 % Favored : 78.25 % 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: 0.14 (0.21), residues: 1677 helix: 1.34 (0.23), residues: 504 sheet: -1.19 (0.22), residues: 474 loop : 0.34 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 365 TYR 0.028 0.002 TYR C 207 PHE 0.012 0.001 PHE Y 67 TRP 0.009 0.001 TRP B 308 HIS 0.009 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00267 (13248) covalent geometry : angle 0.54400 (17967) SS BOND : bond 0.00103 ( 18) SS BOND : angle 0.61069 ( 36) hydrogen bonds : bond 0.03387 ( 523) hydrogen bonds : angle 4.77193 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 321 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8082 (ttt-90) cc_final: 0.7772 (ttt-90) REVERT: A 84 ASP cc_start: 0.8161 (m-30) cc_final: 0.7839 (m-30) REVERT: A 357 SER cc_start: 0.8051 (p) cc_final: 0.7746 (p) REVERT: A 402 ASN cc_start: 0.7440 (m-40) cc_final: 0.7101 (m-40) REVERT: A 422 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 73 ARG cc_start: 0.8117 (ttt-90) cc_final: 0.7854 (ttt180) REVERT: B 84 ASP cc_start: 0.7972 (m-30) cc_final: 0.7740 (m-30) REVERT: B 231 ILE cc_start: 0.8255 (mt) cc_final: 0.7968 (mp) REVERT: B 281 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7891 (mtp85) REVERT: B 323 LEU cc_start: 0.8190 (tp) cc_final: 0.7825 (tt) REVERT: B 353 GLU cc_start: 0.7405 (tp30) cc_final: 0.6882 (tp30) REVERT: W 105 TYR cc_start: 0.8565 (m-80) cc_final: 0.8189 (m-80) REVERT: C 22 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7806 (mm) REVERT: C 227 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8172 (mtpp) REVERT: C 255 ASP cc_start: 0.8150 (m-30) cc_final: 0.7915 (m-30) REVERT: C 357 SER cc_start: 0.8126 (p) cc_final: 0.7902 (p) REVERT: C 422 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 462 LYS cc_start: 0.8042 (tppp) cc_final: 0.7747 (tppp) REVERT: U 27 SER cc_start: 0.8247 (t) cc_final: 0.7930 (p) REVERT: U 29 SER cc_start: 0.8464 (p) cc_final: 0.8156 (m) outliers start: 34 outliers final: 19 residues processed: 334 average time/residue: 0.7041 time to fit residues: 253.5219 Evaluate side-chains 337 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN A 362 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN B 407 GLN B 418 ASN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN C 399 ASN C 407 GLN U 103 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.143621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120835 restraints weight = 18310.869| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.12 r_work: 0.3388 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13266 Z= 0.201 Angle : 0.627 13.985 18003 Z= 0.314 Chirality : 0.046 0.239 2136 Planarity : 0.004 0.051 2307 Dihedral : 4.754 24.462 1824 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 19.77 % Favored : 78.19 % 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: 0.07 (0.21), residues: 1677 helix: 1.28 (0.23), residues: 504 sheet: -1.20 (0.22), residues: 474 loop : 0.28 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 66 TYR 0.025 0.002 TYR B 207 PHE 0.019 0.002 PHE Y 67 TRP 0.008 0.001 TRP C 308 HIS 0.008 0.002 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00498 (13248) covalent geometry : angle 0.62511 (17967) SS BOND : bond 0.00208 ( 18) SS BOND : angle 1.25525 ( 36) hydrogen bonds : bond 0.03737 ( 523) hydrogen bonds : angle 4.88326 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 319 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8020 (ttt-90) cc_final: 0.7735 (ttt-90) REVERT: A 84 ASP cc_start: 0.8126 (m-30) cc_final: 0.7824 (m-30) REVERT: A 231 ILE cc_start: 0.8056 (mt) cc_final: 0.7851 (mp) REVERT: A 357 SER cc_start: 0.8098 (p) cc_final: 0.7790 (p) REVERT: A 362 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8135 (mm110) REVERT: A 393 THR cc_start: 0.8461 (p) cc_final: 0.8110 (p) REVERT: A 402 ASN cc_start: 0.7496 (m-40) cc_final: 0.7218 (m-40) REVERT: A 422 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B 73 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7847 (ttt180) REVERT: B 84 ASP cc_start: 0.7922 (m-30) cc_final: 0.7557 (m-30) REVERT: B 87 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7460 (ttm110) REVERT: B 231 ILE cc_start: 0.8331 (mt) cc_final: 0.8034 (mp) REVERT: B 281 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7967 (mtp85) REVERT: B 323 LEU cc_start: 0.8243 (tp) cc_final: 0.7899 (tt) REVERT: B 353 GLU cc_start: 0.7432 (tp30) cc_final: 0.6910 (tp30) REVERT: B 359 ASN cc_start: 0.8460 (t0) cc_final: 0.8090 (t0) REVERT: B 397 ILE cc_start: 0.7873 (mm) cc_final: 0.7570 (mm) REVERT: W 105 TYR cc_start: 0.8575 (m-80) cc_final: 0.8141 (m-80) REVERT: C 22 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7777 (mm) REVERT: C 69 LYS cc_start: 0.7825 (ttmp) cc_final: 0.7576 (ttmm) REVERT: C 227 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8221 (mtpp) REVERT: C 255 ASP cc_start: 0.8130 (m-30) cc_final: 0.7891 (m-30) REVERT: C 319 LYS cc_start: 0.8415 (mtpm) cc_final: 0.8099 (mtmm) REVERT: C 357 SER cc_start: 0.8115 (p) cc_final: 0.7911 (p) REVERT: C 397 ILE cc_start: 0.7748 (mm) cc_final: 0.7468 (mm) REVERT: C 422 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7953 (mt) REVERT: C 462 LYS cc_start: 0.8036 (tppp) cc_final: 0.7742 (tppp) REVERT: U 29 SER cc_start: 0.8487 (p) cc_final: 0.8243 (m) outliers start: 30 outliers final: 16 residues processed: 331 average time/residue: 0.6910 time to fit residues: 246.7838 Evaluate side-chains 337 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 317 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 107 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN C 70 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 407 GLN U 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121067 restraints weight = 18184.858| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.11 r_work: 0.3394 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13266 Z= 0.192 Angle : 0.838 59.195 18003 Z= 0.466 Chirality : 0.046 0.379 2136 Planarity : 0.004 0.051 2307 Dihedral : 4.752 24.600 1824 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.77 % Allowed : 20.25 % Favored : 77.98 % Cbeta Deviations : 0.06 % 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: 0.07 (0.21), residues: 1677 helix: 1.28 (0.23), residues: 504 sheet: -1.21 (0.22), residues: 474 loop : 0.28 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 365 TYR 0.022 0.002 TYR B 207 PHE 0.015 0.001 PHE Y 67 TRP 0.008 0.001 TRP A 473 HIS 0.008 0.002 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00442 (13248) covalent geometry : angle 0.83376 (17967) SS BOND : bond 0.00156 ( 18) SS BOND : angle 2.12073 ( 36) hydrogen bonds : bond 0.03721 ( 523) hydrogen bonds : angle 4.88164 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5753.22 seconds wall clock time: 98 minutes 48.89 seconds (5928.89 seconds total)