Starting phenix.real_space_refine on Mon Jan 20 10:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5a_42981/01_2025/8v5a_42981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5a_42981/01_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_42981/01_2025/8v5a_42981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5a_42981/01_2025/8v5a_42981.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5a_42981/01_2025/8v5a_42981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5a_42981/01_2025/8v5a_42981.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: "U" 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: W, Y, C, B Time building chain proxies: 8.53, per 1000 atoms: 0.65 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=6, 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 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: 2.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.43 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: 4.26 Time building geometry restraints manager: 3.36 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: 7480 17.54 - 35.08: 475 35.08 - 52.62: 88 52.62 - 70.16: 15 70.16 - 87.70: 18 Dihedral angle restraints: 8076 sinusoidal: 3189 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 8073 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: 2.02 - 2.60: 112 2.60 - 3.17: 11604 3.17 - 3.75: 19898 3.75 - 4.32: 28625 4.32 - 4.90: 47623 Nonbonded interactions: 107862 Sorted by model distance: nonbonded pdb=" SG CYS C 331 " pdb=" SG CYS C 340 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 331 " pdb=" SG CYS B 340 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 355 " pdb=" SG CYS B 363 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 355 " pdb=" SG CYS C 363 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " model vdw 2.031 3.760 ... (remaining 107857 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: 0.08 Found NCS groups: ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.950 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.510 ------------------------------------------------------------------------------- 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 13248 Z= 0.553 Angle : 1.045 8.992 17967 Z= 0.579 Chirality : 0.064 0.330 2136 Planarity : 0.007 0.110 2307 Dihedral : 13.034 87.697 4920 Min Nonbonded Distance : 2.024 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (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 TRP 0.032 0.005 TRP C 308 HIS 0.015 0.005 HIS C 350 PHE 0.024 0.004 PHE W 67 TYR 0.042 0.006 TYR A 438 ARG 0.016 0.003 ARG A 77 *********************** 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 : 1.438 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: 1.3661 time to fit residues: 500.5198 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 : 1.593 ------------------------------------------------------------------------------- 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 141 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 152 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 Y 111 GLN ** 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 ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 395 ASN U 111 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120649 restraints weight = 18446.689| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.12 r_work: 0.3394 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13248 Z= 0.276 Angle : 0.669 7.448 17967 Z= 0.353 Chirality : 0.047 0.150 2136 Planarity : 0.005 0.072 2307 Dihedral : 5.591 29.617 1834 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.39 % Allowed : 9.34 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1677 helix: 0.49 (0.22), residues: 495 sheet: -0.40 (0.24), residues: 411 loop : 0.06 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 308 HIS 0.006 0.002 HIS A 350 PHE 0.017 0.002 PHE U 67 TYR 0.021 0.002 TYR C 48 ARG 0.005 0.001 ARG B 87 *********************** 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 374 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 339 time to evaluate : 1.349 Fit side-chains REVERT: A 73 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7725 (ttt-90) REVERT: A 90 LYS cc_start: 0.6618 (mppt) cc_final: 0.6186 (mppt) REVERT: A 362 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8004 (mm110) REVERT: A 422 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7984 (mt) REVERT: A 472 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7313 (mm-30) REVERT: Y 29 SER cc_start: 0.8502 (p) cc_final: 0.8278 (m) REVERT: Y 31 ILE cc_start: 0.8475 (mm) cc_final: 0.8260 (mp) REVERT: B 73 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7928 (ttt180) REVERT: B 87 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7391 (ttm110) REVERT: B 256 LEU cc_start: 0.8354 (mt) cc_final: 0.8103 (mp) REVERT: B 319 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7955 (ttpt) REVERT: B 323 LEU cc_start: 0.8244 (tp) cc_final: 0.7762 (tt) REVERT: B 353 GLU cc_start: 0.7133 (tp30) cc_final: 0.6636 (tp30) REVERT: B 359 ASN cc_start: 0.8649 (t0) cc_final: 0.8439 (t0) REVERT: B 415 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8485 (mmpt) REVERT: B 422 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8050 (mt) REVERT: W 29 SER cc_start: 0.8430 (p) cc_final: 0.8179 (m) REVERT: C 24 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8184 (mtpt) REVERT: C 295 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8179 (mtpp) REVERT: C 413 THR cc_start: 0.8600 (p) cc_final: 0.8370 (m) REVERT: C 422 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7903 (mt) REVERT: C 464 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8137 (mtmp) REVERT: C 471 LYS cc_start: 0.8196 (mttm) cc_final: 0.7982 (mtpt) outliers start: 35 outliers final: 13 residues processed: 345 average time/residue: 1.3625 time to fit residues: 508.2858 Evaluate side-chains 328 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 312 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 359 ASN A 399 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 395 ASN 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 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 = 0.3839 r_free = 0.3839 target = 0.143636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120828 restraints weight = 18454.125| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.14 r_work: 0.3397 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13248 Z= 0.232 Angle : 0.595 7.528 17967 Z= 0.309 Chirality : 0.044 0.143 2136 Planarity : 0.004 0.062 2307 Dihedral : 5.024 21.795 1826 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.00 % Allowed : 12.41 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1677 helix: 0.85 (0.23), residues: 501 sheet: -0.80 (0.22), residues: 456 loop : 0.27 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 106 HIS 0.005 0.001 HIS C 350 PHE 0.011 0.001 PHE C 427 TYR 0.019 0.002 TYR A 48 ARG 0.003 0.000 ARG B 87 *********************** 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 373 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 1.359 Fit side-chains REVERT: A 22 ILE cc_start: 0.8186 (mt) cc_final: 0.7921 (mm) REVERT: A 23 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 84 ASP cc_start: 0.8226 (m-30) cc_final: 0.7918 (m-30) REVERT: A 88 LEU cc_start: 0.8498 (mp) cc_final: 0.8291 (mp) REVERT: A 90 LYS cc_start: 0.6461 (mppt) cc_final: 0.6222 (mppt) REVERT: A 148 LYS cc_start: 0.8113 (mttt) cc_final: 0.7867 (mtpt) REVERT: A 224 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7882 (mtmt) REVERT: A 362 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7990 (mm110) REVERT: A 422 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 472 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7287 (mm-30) REVERT: Y 31 ILE cc_start: 0.8496 (mm) cc_final: 0.8265 (mp) REVERT: B 23 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8290 (m) REVERT: B 73 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7921 (ttt180) REVERT: B 281 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7976 (mtp85) REVERT: B 319 LYS cc_start: 0.8259 (mtpp) cc_final: 0.8000 (ttpp) REVERT: B 323 LEU cc_start: 0.8217 (tp) cc_final: 0.7781 (tt) REVERT: B 353 GLU cc_start: 0.7218 (tp30) cc_final: 0.6651 (tp30) REVERT: B 415 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8534 (mmpt) REVERT: B 422 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8071 (mt) REVERT: W 29 SER cc_start: 0.8389 (p) cc_final: 0.8156 (m) REVERT: C 69 LYS cc_start: 0.7699 (tptp) cc_final: 0.7399 (ttmm) REVERT: C 319 LYS cc_start: 0.8311 (mtpm) cc_final: 0.7992 (mtmm) REVERT: C 413 THR cc_start: 0.8633 (p) cc_final: 0.8358 (m) REVERT: C 422 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7938 (mt) REVERT: C 459 GLU cc_start: 0.7892 (pt0) cc_final: 0.7681 (pt0) REVERT: C 462 LYS cc_start: 0.8127 (tppp) cc_final: 0.7899 (tppp) REVERT: U 32 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8413 (ttmm) outliers start: 44 outliers final: 12 residues processed: 339 average time/residue: 1.3561 time to fit residues: 498.1508 Evaluate side-chains 350 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 331 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 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 281 ARG 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 W residue 25 SER Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 32 LYS 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 44 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 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 127 GLN A 162 GLN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 407 GLN W 111 GLN C 127 GLN ** C 162 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 272 ASN C 350 HIS C 359 ASN C 399 ASN U 103 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119142 restraints weight = 18324.403| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.11 r_work: 0.3376 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13248 Z= 0.317 Angle : 0.601 7.023 17967 Z= 0.311 Chirality : 0.045 0.143 2136 Planarity : 0.004 0.060 2307 Dihedral : 5.041 21.681 1824 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.68 % Allowed : 13.50 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1677 helix: 0.90 (0.23), residues: 501 sheet: -1.06 (0.22), residues: 474 loop : 0.24 (0.26), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 106 HIS 0.003 0.001 HIS A 315 PHE 0.014 0.002 PHE C 427 TYR 0.019 0.002 TYR A 207 ARG 0.006 0.000 ARG B 87 *********************** 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 378 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7891 (mm) REVERT: A 23 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8197 (m) REVERT: A 73 ARG cc_start: 0.8094 (ttt-90) cc_final: 0.7830 (ttt-90) REVERT: A 148 LYS cc_start: 0.8204 (mttt) cc_final: 0.7888 (mtpt) REVERT: A 362 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8044 (mm110) REVERT: A 402 ASN cc_start: 0.7479 (m-40) cc_final: 0.7199 (m-40) REVERT: A 422 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8098 (mt) REVERT: A 472 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 23 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8270 (m) REVERT: B 73 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7888 (ttt180) REVERT: B 281 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7976 (mtp85) REVERT: B 319 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7975 (ttpt) REVERT: B 323 LEU cc_start: 0.8249 (tp) cc_final: 0.7782 (tt) REVERT: B 353 GLU cc_start: 0.7277 (tp30) cc_final: 0.6685 (tp30) REVERT: B 422 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8093 (mt) REVERT: W 29 SER cc_start: 0.8452 (p) cc_final: 0.8216 (m) REVERT: C 69 LYS cc_start: 0.7693 (tptp) cc_final: 0.7430 (ttmm) REVERT: C 319 LYS cc_start: 0.8338 (mtpm) cc_final: 0.8011 (mtmm) REVERT: C 357 SER cc_start: 0.8131 (p) cc_final: 0.7922 (p) REVERT: C 413 THR cc_start: 0.8591 (p) cc_final: 0.8328 (m) REVERT: C 422 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7948 (mt) REVERT: C 462 LYS cc_start: 0.8127 (tppp) cc_final: 0.7879 (tppp) REVERT: U 29 SER cc_start: 0.8439 (p) cc_final: 0.8217 (m) REVERT: U 32 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8417 (ttmm) outliers start: 54 outliers final: 19 residues processed: 343 average time/residue: 1.3188 time to fit residues: 491.4544 Evaluate side-chains 354 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE 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 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 25 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL 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 W residue 25 SER Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 63 CYS 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 422 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 36 optimal weight: 0.0570 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 407 GLN B 162 GLN B 292 GLN 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 292 GLN 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 = 0.3836 r_free = 0.3836 target = 0.143228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120495 restraints weight = 18509.406| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.15 r_work: 0.3390 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13248 Z= 0.228 Angle : 0.563 6.995 17967 Z= 0.290 Chirality : 0.044 0.133 2136 Planarity : 0.004 0.054 2307 Dihedral : 4.842 21.279 1824 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.68 % Allowed : 15.00 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1677 helix: 1.01 (0.23), residues: 501 sheet: -1.05 (0.22), residues: 474 loop : 0.23 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 106 HIS 0.007 0.001 HIS C 350 PHE 0.010 0.001 PHE C 427 TYR 0.022 0.002 TYR C 48 ARG 0.004 0.000 ARG A 265 *********************** 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 391 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 1.355 Fit side-chains REVERT: A 23 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8164 (m) REVERT: A 73 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.7817 (ttt-90) REVERT: A 148 LYS cc_start: 0.8191 (mttt) cc_final: 0.7724 (mtpt) REVERT: A 362 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8039 (mm110) REVERT: A 402 ASN cc_start: 0.7477 (m-40) cc_final: 0.7159 (m-40) REVERT: A 422 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 472 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 23 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8221 (m) REVERT: B 73 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7857 (ttt180) REVERT: B 281 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7884 (mtp85) REVERT: B 287 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7439 (mmm-85) REVERT: B 319 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8042 (mtpp) REVERT: B 323 LEU cc_start: 0.8247 (tp) cc_final: 0.7796 (tt) REVERT: B 353 GLU cc_start: 0.7311 (tp30) cc_final: 0.6701 (tp30) REVERT: B 422 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8062 (mt) REVERT: W 29 SER cc_start: 0.8391 (p) cc_final: 0.8134 (m) REVERT: W 105 TYR cc_start: 0.8557 (m-80) cc_final: 0.8218 (m-80) REVERT: C 39 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8063 (mtmt) REVERT: C 69 LYS cc_start: 0.7698 (tptp) cc_final: 0.7423 (ttmm) REVERT: C 305 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8509 (m-40) REVERT: C 319 LYS cc_start: 0.8330 (mtpm) cc_final: 0.8002 (mtmm) REVERT: C 413 THR cc_start: 0.8630 (p) cc_final: 0.8329 (m) REVERT: C 422 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7935 (mt) REVERT: C 462 LYS cc_start: 0.8112 (tppp) cc_final: 0.7815 (tppp) REVERT: U 27 SER cc_start: 0.8260 (t) cc_final: 0.7896 (p) REVERT: U 29 SER cc_start: 0.8443 (p) cc_final: 0.8166 (m) outliers start: 54 outliers final: 20 residues processed: 354 average time/residue: 1.2806 time to fit residues: 492.8675 Evaluate side-chains 354 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 B residue 23 THR Chi-restraints excluded: chain B residue 63 CYS 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 420 ILE Chi-restraints excluded: chain B residue 422 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 C residue 39 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 305 ASN 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 C residue 474 ILE Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 69 optimal weight: 0.1980 chunk 123 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 130 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 96 optimal weight: 0.0770 chunk 150 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 160 optimal weight: 0.6980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 395 ASN A 407 GLN A 418 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 292 GLN C 399 ASN C 461 ASN U 103 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122367 restraints weight = 18627.353| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.16 r_work: 0.3416 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13248 Z= 0.155 Angle : 0.538 7.177 17967 Z= 0.276 Chirality : 0.043 0.129 2136 Planarity : 0.004 0.049 2307 Dihedral : 4.627 19.586 1824 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.27 % Allowed : 16.50 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1677 helix: 1.14 (0.23), residues: 504 sheet: -1.15 (0.22), residues: 474 loop : 0.30 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 308 HIS 0.008 0.001 HIS C 350 PHE 0.007 0.001 PHE Y 67 TYR 0.023 0.002 TYR C 207 ARG 0.004 0.000 ARG A 265 *********************** 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 375 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7830 (ttt-90) REVERT: A 84 ASP cc_start: 0.8179 (m-30) cc_final: 0.7864 (m-30) REVERT: A 362 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8002 (mm110) REVERT: A 402 ASN cc_start: 0.7487 (m-40) cc_final: 0.7146 (m-40) REVERT: A 422 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 73 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7846 (ttt180) REVERT: B 281 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7887 (mtp85) REVERT: B 287 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7409 (mmm-85) REVERT: B 319 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7969 (mtpp) REVERT: B 323 LEU cc_start: 0.8205 (tp) cc_final: 0.7786 (tt) REVERT: B 353 GLU cc_start: 0.7326 (tp30) cc_final: 0.6771 (tp30) REVERT: B 422 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8003 (mt) REVERT: W 105 TYR cc_start: 0.8550 (m-80) cc_final: 0.8182 (m-80) REVERT: C 39 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8098 (mtmt) REVERT: C 69 LYS cc_start: 0.7728 (tptp) cc_final: 0.7460 (ttmm) REVERT: C 88 LEU cc_start: 0.8522 (mp) cc_final: 0.8307 (mp) REVERT: C 255 ASP cc_start: 0.8151 (m-30) cc_final: 0.7931 (m-30) REVERT: C 305 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8507 (m-40) REVERT: C 319 LYS cc_start: 0.8344 (mtpm) cc_final: 0.8026 (mtmm) REVERT: C 375 ARG cc_start: 0.8626 (mpt180) cc_final: 0.8418 (mpt180) REVERT: C 422 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7915 (mt) REVERT: C 462 LYS cc_start: 0.8066 (tppp) cc_final: 0.7804 (tppp) REVERT: U 27 SER cc_start: 0.8196 (t) cc_final: 0.7917 (p) REVERT: U 29 SER cc_start: 0.8357 (p) cc_final: 0.8052 (m) outliers start: 48 outliers final: 17 residues processed: 346 average time/residue: 1.3574 time to fit residues: 508.1807 Evaluate side-chains 344 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 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 C residue 39 LYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 305 ASN 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 99 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 0.0670 chunk 85 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 161 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 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 198 GLN C 292 GLN ** 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 = 0.3838 r_free = 0.3838 target = 0.143635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121003 restraints weight = 18533.149| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.15 r_work: 0.3403 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13248 Z= 0.229 Angle : 0.566 10.404 17967 Z= 0.287 Chirality : 0.043 0.127 2136 Planarity : 0.004 0.050 2307 Dihedral : 4.640 20.124 1824 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 17.86 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1677 helix: 1.22 (0.23), residues: 504 sheet: -1.18 (0.22), residues: 474 loop : 0.30 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 106 HIS 0.010 0.001 HIS C 350 PHE 0.010 0.001 PHE U 67 TYR 0.025 0.002 TYR C 207 ARG 0.006 0.000 ARG C 87 *********************** 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 358 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7838 (ttt-90) REVERT: A 84 ASP cc_start: 0.8204 (m-30) cc_final: 0.7865 (m-30) REVERT: A 161 VAL cc_start: 0.6142 (OUTLIER) cc_final: 0.5892 (m) REVERT: A 307 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 362 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8083 (mm110) REVERT: A 402 ASN cc_start: 0.7468 (m-40) cc_final: 0.7187 (m-40) REVERT: A 422 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 73 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7876 (ttt180) REVERT: B 231 ILE cc_start: 0.8353 (mt) cc_final: 0.8061 (mp) REVERT: B 281 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7907 (mtp85) REVERT: B 319 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7983 (mtpp) REVERT: B 323 LEU cc_start: 0.8249 (tp) cc_final: 0.7889 (tt) REVERT: B 353 GLU cc_start: 0.7392 (tp30) cc_final: 0.6865 (tp30) REVERT: B 422 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8064 (mt) REVERT: W 105 TYR cc_start: 0.8571 (m-80) cc_final: 0.8240 (m-80) REVERT: C 69 LYS cc_start: 0.7731 (tptp) cc_final: 0.7467 (ttmm) REVERT: C 87 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7644 (ttp80) REVERT: C 255 ASP cc_start: 0.8134 (m-30) cc_final: 0.7910 (m-30) REVERT: C 319 LYS cc_start: 0.8354 (mtpm) cc_final: 0.8024 (mtmm) REVERT: C 422 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7949 (mt) REVERT: C 462 LYS cc_start: 0.8075 (tppp) cc_final: 0.7802 (tppp) REVERT: U 27 SER cc_start: 0.8278 (t) cc_final: 0.7914 (p) REVERT: U 29 SER cc_start: 0.8384 (p) cc_final: 0.8099 (m) outliers start: 40 outliers final: 20 residues processed: 332 average time/residue: 1.3972 time to fit residues: 503.4559 Evaluate side-chains 339 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 314 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 226 ILE 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 25 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 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 C residue 63 CYS 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 359 ASN Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 115 optimal weight: 0.0020 chunk 149 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 A 461 ASN ** 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 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120938 restraints weight = 18521.806| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.13 r_work: 0.3398 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13248 Z= 0.229 Angle : 0.564 9.069 17967 Z= 0.287 Chirality : 0.044 0.130 2136 Planarity : 0.004 0.049 2307 Dihedral : 4.644 19.899 1824 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.34 % Allowed : 17.79 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1677 helix: 1.26 (0.23), residues: 504 sheet: -1.20 (0.22), residues: 474 loop : 0.31 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 106 HIS 0.009 0.001 HIS C 350 PHE 0.012 0.001 PHE U 67 TYR 0.026 0.002 TYR C 207 ARG 0.004 0.000 ARG C 87 *********************** 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 360 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8070 (ttt-90) cc_final: 0.7813 (ttt-90) REVERT: A 84 ASP cc_start: 0.8186 (m-30) cc_final: 0.7863 (m-30) REVERT: A 161 VAL cc_start: 0.5330 (OUTLIER) cc_final: 0.5126 (m) REVERT: A 361 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8469 (m) REVERT: A 362 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8060 (mm110) REVERT: A 402 ASN cc_start: 0.7461 (m-40) cc_final: 0.7178 (m-40) REVERT: A 422 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 73 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7849 (ttt180) REVERT: B 231 ILE cc_start: 0.8333 (mt) cc_final: 0.8044 (mp) REVERT: B 281 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7855 (mtp85) REVERT: B 323 LEU cc_start: 0.8251 (tp) cc_final: 0.7892 (tt) REVERT: B 353 GLU cc_start: 0.7409 (tp30) cc_final: 0.6905 (tp30) REVERT: B 397 ILE cc_start: 0.7828 (mm) cc_final: 0.7523 (mm) REVERT: B 422 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8063 (mt) REVERT: W 105 TYR cc_start: 0.8576 (m-80) cc_final: 0.8229 (m-80) REVERT: C 69 LYS cc_start: 0.7701 (tptp) cc_final: 0.7430 (ttmm) REVERT: C 87 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7616 (ttp80) REVERT: C 88 LEU cc_start: 0.8510 (mp) cc_final: 0.8262 (mp) REVERT: C 255 ASP cc_start: 0.8130 (m-30) cc_final: 0.7906 (m-30) REVERT: C 319 LYS cc_start: 0.8342 (mtpm) cc_final: 0.8011 (mtmm) REVERT: C 375 ARG cc_start: 0.8737 (mpt180) cc_final: 0.8511 (mpt180) REVERT: C 422 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7970 (mt) REVERT: C 462 LYS cc_start: 0.8076 (tppp) cc_final: 0.7806 (tppp) REVERT: U 29 SER cc_start: 0.8401 (p) cc_final: 0.8147 (m) outliers start: 49 outliers final: 24 residues processed: 330 average time/residue: 1.3742 time to fit residues: 490.9793 Evaluate side-chains 342 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 226 ILE 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 361 SER 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 25 SER Chi-restraints excluded: chain B residue 63 CYS 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 357 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 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 C residue 63 CYS 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 99 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 13 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ** 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 350 HIS 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 = 0.3845 r_free = 0.3845 target = 0.144076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121272 restraints weight = 18291.999| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.13 r_work: 0.3404 rms_B_bonded: 2.76 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: 0.7616 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 : 0.003 0.040 13248 Z= 0.224 Angle : 0.565 10.156 17967 Z= 0.286 Chirality : 0.044 0.151 2136 Planarity : 0.004 0.048 2307 Dihedral : 4.586 19.176 1824 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.14 % Allowed : 18.27 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1677 helix: 1.32 (0.23), residues: 504 sheet: -1.24 (0.22), residues: 474 loop : 0.33 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 308 HIS 0.010 0.001 HIS C 350 PHE 0.010 0.001 PHE U 67 TYR 0.030 0.002 TYR C 207 ARG 0.004 0.000 ARG C 87 *********************** 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 359 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 22 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7866 (mm) REVERT: A 45 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 73 ARG cc_start: 0.8035 (ttt-90) cc_final: 0.7767 (ttt-90) REVERT: A 84 ASP cc_start: 0.8155 (m-30) cc_final: 0.7830 (m-30) REVERT: A 362 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8141 (mm110) REVERT: A 402 ASN cc_start: 0.7474 (m-40) cc_final: 0.7186 (m-40) REVERT: A 422 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8124 (mt) REVERT: B 73 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7832 (ttt180) REVERT: B 231 ILE cc_start: 0.8229 (mt) cc_final: 0.7936 (mp) REVERT: B 281 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7857 (mtp85) REVERT: B 397 ILE cc_start: 0.7823 (mm) cc_final: 0.7513 (mm) REVERT: B 422 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (mt) REVERT: W 105 TYR cc_start: 0.8581 (m-80) cc_final: 0.8173 (m-80) REVERT: C 69 LYS cc_start: 0.7690 (tptp) cc_final: 0.7393 (ttmm) REVERT: C 87 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7547 (ttp80) REVERT: C 88 LEU cc_start: 0.8465 (mp) cc_final: 0.8203 (mp) REVERT: C 148 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7804 (mmmm) REVERT: C 255 ASP cc_start: 0.8097 (m-30) cc_final: 0.7854 (m-30) REVERT: C 319 LYS cc_start: 0.8331 (mtpm) cc_final: 0.7993 (mtmm) REVERT: C 419 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8121 (t) REVERT: C 422 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7954 (mt) REVERT: C 462 LYS cc_start: 0.8021 (tppp) cc_final: 0.7751 (tppp) REVERT: U 29 SER cc_start: 0.8396 (p) cc_final: 0.8133 (m) outliers start: 46 outliers final: 23 residues processed: 333 average time/residue: 1.3609 time to fit residues: 490.5811 Evaluate side-chains 339 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 ILE 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 25 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 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 C residue 63 CYS Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 161 VAL 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 419 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 A 407 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 386 ASN B 402 ASN 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 292 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN 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 = 0.3846 r_free = 0.3846 target = 0.144294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121478 restraints weight = 18316.995| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.13 r_work: 0.3402 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.004 0.119 13248 Z= 0.269 Angle : 0.798 59.200 17967 Z= 0.448 Chirality : 0.044 0.143 2136 Planarity : 0.004 0.048 2307 Dihedral : 4.582 19.419 1824 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.18 % Allowed : 19.43 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1677 helix: 1.31 (0.23), residues: 504 sheet: -1.23 (0.22), residues: 474 loop : 0.34 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 308 HIS 0.010 0.001 HIS C 350 PHE 0.027 0.002 PHE Y 67 TYR 0.029 0.002 TYR C 207 ARG 0.003 0.000 ARG U 66 ********************** 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 339 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 307 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 73 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7762 (ttt-90) REVERT: A 84 ASP cc_start: 0.8152 (m-30) cc_final: 0.7834 (m-30) REVERT: A 362 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8074 (mm-40) REVERT: A 402 ASN cc_start: 0.7473 (m-40) cc_final: 0.7186 (m-40) REVERT: A 422 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 73 ARG cc_start: 0.8105 (ttt-90) cc_final: 0.7834 (ttt180) REVERT: B 231 ILE cc_start: 0.8226 (mt) cc_final: 0.7939 (mp) REVERT: B 281 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7846 (mtp85) REVERT: B 359 ASN cc_start: 0.8387 (t0) cc_final: 0.8040 (t160) REVERT: B 397 ILE cc_start: 0.7836 (mm) cc_final: 0.7525 (mm) REVERT: B 422 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8041 (mt) REVERT: W 105 TYR cc_start: 0.8591 (m-80) cc_final: 0.8174 (m-80) REVERT: C 69 LYS cc_start: 0.7687 (tptp) cc_final: 0.7395 (ttmm) REVERT: C 87 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7534 (ttp80) REVERT: C 88 LEU cc_start: 0.8465 (mp) cc_final: 0.8196 (mp) REVERT: C 148 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7804 (mmmm) REVERT: C 255 ASP cc_start: 0.8105 (m-30) cc_final: 0.7858 (m-30) REVERT: C 319 LYS cc_start: 0.8342 (mtpm) cc_final: 0.8003 (mtmm) REVERT: C 419 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (t) REVERT: C 422 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7961 (mt) REVERT: C 462 LYS cc_start: 0.8025 (tppp) cc_final: 0.7759 (tppp) REVERT: U 29 SER cc_start: 0.8398 (p) cc_final: 0.8136 (m) outliers start: 32 outliers final: 22 residues processed: 322 average time/residue: 1.3559 time to fit residues: 472.3220 Evaluate side-chains 337 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 296 VAL 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 Y residue 25 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 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 C residue 63 CYS Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 161 VAL 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 419 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 126 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 407 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 386 ASN 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 292 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.144585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121601 restraints weight = 18505.574| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.15 r_work: 0.3400 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13248 Z= 0.226 Angle : 0.584 11.222 17967 Z= 0.292 Chirality : 0.044 0.157 2136 Planarity : 0.004 0.048 2307 Dihedral : 4.572 19.338 1824 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.39 % Allowed : 19.02 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1677 helix: 1.33 (0.23), residues: 504 sheet: -1.24 (0.22), residues: 474 loop : 0.34 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 308 HIS 0.009 0.001 HIS C 350 PHE 0.040 0.001 PHE Y 67 TYR 0.029 0.002 TYR C 207 ARG 0.006 0.000 ARG B 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11379.70 seconds wall clock time: 200 minutes 51.62 seconds (12051.62 seconds total)