Starting phenix.real_space_refine on Fri Sep 27 05:40:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/09_2024/8v5a_42981.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/09_2024/8v5a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/09_2024/8v5a_42981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/09_2024/8v5a_42981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/09_2024/8v5a_42981.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v5a_42981/09_2024/8v5a_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-5461/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: 8.59, per 1000 atoms: 0.66 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: 2.87 Conformation dependent library (CDL) restraints added in 1.6 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: 1.56 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: 4.04 Time building geometry restraints manager: 3.44 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'Y' } 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: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 31.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.520 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: 1.2860 time to fit residues: 472.1144 Evaluate side-chains 325 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 320 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 fitting. rotamer outliers: 35 poor density : 339 time to evaluate : 1.395 Fit side-chains REVERT: A 90 LYS cc_start: 0.5961 (mppt) cc_final: 0.5616 (mppt) REVERT: A 362 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7391 (mm110) REVERT: A 422 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7524 (mt) REVERT: B 353 GLU cc_start: 0.6470 (tp30) cc_final: 0.6177 (tp30) REVERT: B 375 ARG cc_start: 0.7652 (mpt180) cc_final: 0.7449 (mpt180) REVERT: B 422 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7474 (mt) REVERT: C 24 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7360 (mtpt) REVERT: C 362 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7317 (mm-40) REVERT: C 413 THR cc_start: 0.7920 (p) cc_final: 0.7649 (m) REVERT: C 422 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7364 (mt) outliers start: 35 outliers final: 13 residues processed: 345 average time/residue: 1.3249 time to fit residues: 494.6360 Evaluate side-chains 335 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 319 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 84 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 359 ASN A 399 ASN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13248 Z= 0.328 Angle : 0.637 7.364 17967 Z= 0.329 Chirality : 0.046 0.166 2136 Planarity : 0.004 0.065 2307 Dihedral : 5.225 22.808 1826 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.68 % Allowed : 12.07 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1677 helix: 0.73 (0.23), residues: 501 sheet: -0.83 (0.22), residues: 456 loop : 0.19 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 106 HIS 0.005 0.002 HIS C 350 PHE 0.015 0.002 PHE C 427 TYR 0.018 0.002 TYR A 48 ARG 0.006 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 392 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 338 time to evaluate : 1.421 Fit side-chains REVERT: A 23 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7762 (m) REVERT: A 224 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7266 (mtmt) REVERT: A 422 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7603 (mt) REVERT: B 23 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7913 (m) REVERT: B 353 GLU cc_start: 0.6627 (tp30) cc_final: 0.6196 (tp30) REVERT: B 422 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7563 (mt) REVERT: C 357 SER cc_start: 0.7464 (p) cc_final: 0.7185 (p) REVERT: C 413 THR cc_start: 0.7940 (p) cc_final: 0.7704 (m) REVERT: C 422 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7465 (mt) outliers start: 54 outliers final: 17 residues processed: 353 average time/residue: 1.3371 time to fit residues: 511.2921 Evaluate side-chains 355 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 46 THR 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 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 153 optimal weight: 0.6980 chunk 162 optimal weight: 0.0270 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 350 HIS A 362 GLN A 407 GLN B 162 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 350 HIS B 407 GLN W 111 GLN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 359 ASN C 399 ASN U 103 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13248 Z= 0.181 Angle : 0.569 7.624 17967 Z= 0.292 Chirality : 0.043 0.128 2136 Planarity : 0.004 0.055 2307 Dihedral : 4.887 21.045 1826 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.27 % Allowed : 15.27 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.21), residues: 1677 helix: 0.97 (0.23), residues: 501 sheet: -1.03 (0.22), residues: 474 loop : 0.26 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 308 HIS 0.006 0.001 HIS C 350 PHE 0.008 0.001 PHE C 427 TYR 0.022 0.002 TYR C 48 ARG 0.005 0.000 ARG A 265 *********************** 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 393 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 345 time to evaluate : 1.491 Fit side-chains REVERT: A 148 LYS cc_start: 0.7581 (mtpt) cc_final: 0.6969 (mtpt) REVERT: A 409 VAL cc_start: 0.8594 (m) cc_final: 0.8330 (t) REVERT: B 23 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7842 (m) REVERT: B 281 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7532 (mtp85) REVERT: B 353 GLU cc_start: 0.6615 (tp30) cc_final: 0.6253 (tp30) REVERT: B 359 ASN cc_start: 0.7935 (t0) cc_final: 0.7711 (t0) REVERT: B 362 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7589 (mm-40) REVERT: B 422 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7497 (mt) REVERT: W 105 TYR cc_start: 0.8163 (m-80) cc_final: 0.7915 (m-80) REVERT: C 413 THR cc_start: 0.8024 (p) cc_final: 0.7678 (m) REVERT: C 422 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (mt) outliers start: 48 outliers final: 14 residues processed: 358 average time/residue: 1.2708 time to fit residues: 493.4264 Evaluate side-chains 353 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 335 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 ILE Chi-restraints excluded: chain A residue 420 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 296 VAL Chi-restraints excluded: chain B residue 360 ILE 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 C residue 474 ILE 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 135 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 40 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 350 HIS A 395 ASN A 418 ASN B 66 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 402 ASN C 127 GLN C 162 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13248 Z= 0.268 Angle : 0.586 6.915 17967 Z= 0.301 Chirality : 0.045 0.176 2136 Planarity : 0.004 0.051 2307 Dihedral : 4.894 21.803 1824 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.82 % Allowed : 15.88 % Favored : 80.30 % 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: -0.03 (0.21), residues: 1677 helix: 1.05 (0.23), residues: 501 sheet: -1.11 (0.22), residues: 474 loop : 0.23 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 106 HIS 0.008 0.001 HIS C 350 PHE 0.011 0.001 PHE C 427 TYR 0.021 0.002 TYR C 207 ARG 0.005 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 395 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 339 time to evaluate : 1.328 Fit side-chains REVERT: A 148 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7341 (mtpt) REVERT: A 362 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7362 (mm110) REVERT: B 23 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (m) REVERT: B 281 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7471 (mtp85) REVERT: B 357 SER cc_start: 0.7732 (p) cc_final: 0.7514 (t) REVERT: B 422 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7514 (mt) REVERT: W 105 TYR cc_start: 0.8160 (m-80) cc_final: 0.7854 (m-80) REVERT: C 227 LYS cc_start: 0.7500 (mtpp) cc_final: 0.7298 (mtpp) REVERT: C 413 THR cc_start: 0.8058 (p) cc_final: 0.7732 (m) REVERT: C 422 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7426 (mt) outliers start: 56 outliers final: 21 residues processed: 360 average time/residue: 1.2559 time to fit residues: 489.9286 Evaluate side-chains 351 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 325 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 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 318 THR 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 63 CYS Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU 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 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 54 optimal weight: 0.8980 chunk 146 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 85 optimal weight: 0.0980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 359 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 292 GLN B 402 ASN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN C 461 ASN U 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13248 Z= 0.194 Angle : 0.553 7.068 17967 Z= 0.283 Chirality : 0.043 0.140 2136 Planarity : 0.003 0.048 2307 Dihedral : 4.706 20.129 1824 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.07 % Allowed : 17.59 % Favored : 79.35 % 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: 1.18 (0.23), residues: 501 sheet: -1.20 (0.22), residues: 474 loop : 0.28 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 106 HIS 0.008 0.001 HIS C 350 PHE 0.008 0.001 PHE U 67 TYR 0.023 0.002 TYR A 207 ARG 0.003 0.000 ARG C 375 *********************** 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 368 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 323 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7142 (mtpt) REVERT: A 362 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7349 (mm110) REVERT: B 23 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7804 (m) REVERT: B 281 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7498 (mtp85) REVERT: B 422 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7479 (mt) REVERT: W 105 TYR cc_start: 0.8163 (m-80) cc_final: 0.7880 (m-80) REVERT: C 39 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7560 (mtmt) REVERT: C 422 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7400 (mt) outliers start: 45 outliers final: 22 residues processed: 341 average time/residue: 1.2855 time to fit residues: 474.9689 Evaluate side-chains 345 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 317 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 161 VAL 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 Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR 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 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 161 VAL Chi-restraints excluded: chain C residue 221 LEU 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 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 156 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 91 optimal weight: 0.3980 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 161 optimal weight: 0.0770 chunk 101 optimal weight: 0.0170 chunk 98 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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 359 ASN A 407 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 386 ASN B 402 ASN C 127 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 399 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13248 Z= 0.166 Angle : 0.549 7.360 17967 Z= 0.279 Chirality : 0.043 0.129 2136 Planarity : 0.003 0.046 2307 Dihedral : 4.573 23.333 1824 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.00 % Allowed : 18.13 % 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: 0.07 (0.21), residues: 1677 helix: 1.29 (0.23), residues: 501 sheet: -1.21 (0.22), residues: 474 loop : 0.28 (0.25), residues: 702 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 0.008 0.001 PHE U 67 TYR 0.024 0.002 TYR C 207 ARG 0.004 0.000 ARG A 73 *********************** 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 359 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 315 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7185 (mtpt) REVERT: B 23 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7777 (m) REVERT: B 231 ILE cc_start: 0.8520 (mt) cc_final: 0.8222 (mp) REVERT: B 281 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7458 (mtp85) REVERT: B 422 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7444 (mt) REVERT: W 105 TYR cc_start: 0.8153 (m-80) cc_final: 0.7889 (m-80) REVERT: C 39 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7545 (mtmt) REVERT: C 422 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7383 (mt) outliers start: 44 outliers final: 19 residues processed: 334 average time/residue: 1.3196 time to fit residues: 480.2739 Evaluate side-chains 337 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 312 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 161 VAL 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 Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR 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 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 C residue 39 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 474 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 100 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN A 362 GLN A 407 GLN A 461 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 359 ASN B 402 ASN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 238 ASN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN U 103 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13248 Z= 0.260 Angle : 0.581 9.496 17967 Z= 0.295 Chirality : 0.044 0.143 2136 Planarity : 0.003 0.047 2307 Dihedral : 4.665 22.541 1824 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 18.61 % Favored : 78.53 % 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: 1.28 (0.23), residues: 501 sheet: -1.24 (0.22), residues: 474 loop : 0.29 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 473 HIS 0.009 0.001 HIS C 350 PHE 0.014 0.001 PHE U 67 TYR 0.026 0.002 TYR C 207 ARG 0.004 0.000 ARG C 375 *********************** 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 357 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 315 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 362 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7330 (mm110) REVERT: B 23 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7789 (m) REVERT: B 231 ILE cc_start: 0.8507 (mt) cc_final: 0.8220 (mp) REVERT: B 281 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7471 (mtp85) REVERT: B 397 ILE cc_start: 0.7470 (mm) cc_final: 0.7237 (mm) REVERT: B 422 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7511 (mt) REVERT: W 105 TYR cc_start: 0.8175 (m-80) cc_final: 0.7848 (m-80) REVERT: C 22 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8001 (mm) REVERT: C 422 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7506 (mt) outliers start: 42 outliers final: 23 residues processed: 332 average time/residue: 1.2851 time to fit residues: 462.2774 Evaluate side-chains 342 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 314 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 63 CYS 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 318 THR Chi-restraints excluded: chain B residue 330 GLU 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 W residue 78 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 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 155 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.0980 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN B 292 GLN B 359 ASN B 402 ASN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 350 HIS C 399 ASN U 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.005 0.055 13248 Z= 0.359 Angle : 0.629 11.267 17967 Z= 0.319 Chirality : 0.047 0.180 2136 Planarity : 0.004 0.048 2307 Dihedral : 4.881 22.801 1824 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.79 % Allowed : 19.09 % Favored : 78.12 % 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: 1.11 (0.23), residues: 504 sheet: -1.30 (0.22), residues: 474 loop : 0.20 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 308 HIS 0.011 0.002 HIS C 350 PHE 0.014 0.002 PHE C 427 TYR 0.031 0.002 TYR C 207 ARG 0.003 0.000 ARG A 73 *********************** 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 349 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 1.271 Fit side-chains REVERT: A 231 ILE cc_start: 0.8348 (mt) cc_final: 0.8146 (mp) REVERT: A 357 SER cc_start: 0.7534 (p) cc_final: 0.7303 (t) REVERT: A 362 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7403 (mm110) REVERT: A 393 THR cc_start: 0.7998 (p) cc_final: 0.7706 (p) REVERT: B 23 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 231 ILE cc_start: 0.8494 (mt) cc_final: 0.8215 (mp) REVERT: B 281 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7493 (mtp85) REVERT: B 397 ILE cc_start: 0.7511 (mm) cc_final: 0.7254 (mm) REVERT: B 422 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7518 (mt) REVERT: C 22 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7850 (mm) REVERT: C 413 THR cc_start: 0.8052 (p) cc_final: 0.7751 (m) REVERT: C 419 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7450 (p) REVERT: C 422 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7604 (mt) outliers start: 41 outliers final: 24 residues processed: 326 average time/residue: 1.2946 time to fit residues: 457.2989 Evaluate side-chains 336 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 306 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR 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 318 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 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain U residue 31 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 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.3980 chunk 154 optimal weight: 0.0970 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 359 ASN A 407 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 359 ASN B 402 ASN B 418 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 399 ASN U 103 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13248 Z= 0.216 Angle : 0.589 11.259 17967 Z= 0.297 Chirality : 0.044 0.147 2136 Planarity : 0.003 0.046 2307 Dihedral : 4.691 21.983 1824 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.25 % Allowed : 19.70 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1677 helix: 1.18 (0.23), residues: 504 sheet: -1.32 (0.22), residues: 474 loop : 0.25 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.009 0.001 HIS C 350 PHE 0.011 0.001 PHE Y 67 TYR 0.030 0.002 TYR A 207 ARG 0.006 0.000 ARG C 375 ********************** 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 346 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 313 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 362 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7274 (mm110) REVERT: B 23 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7772 (m) REVERT: B 231 ILE cc_start: 0.8472 (mt) cc_final: 0.8178 (mp) REVERT: B 281 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7443 (mtp85) REVERT: B 397 ILE cc_start: 0.7518 (mm) cc_final: 0.7266 (mm) REVERT: B 422 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7516 (mt) REVERT: C 22 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7802 (mm) REVERT: C 413 THR cc_start: 0.8058 (p) cc_final: 0.7755 (m) REVERT: C 419 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7409 (p) outliers start: 33 outliers final: 19 residues processed: 329 average time/residue: 1.2546 time to fit residues: 447.8615 Evaluate side-chains 335 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 30 THR 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 296 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 419 THR 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 40 optimal weight: 0.0870 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 359 ASN B 292 GLN B 402 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120990 restraints weight = 18086.255| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.13 r_work: 0.3401 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13248 Z= 0.251 Angle : 0.595 13.650 17967 Z= 0.300 Chirality : 0.044 0.174 2136 Planarity : 0.003 0.046 2307 Dihedral : 4.697 21.454 1824 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.11 % Allowed : 20.04 % Favored : 77.85 % 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: -0.03 (0.21), residues: 1677 helix: 1.19 (0.23), residues: 504 sheet: -1.33 (0.22), residues: 474 loop : 0.27 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 308 HIS 0.008 0.001 HIS C 350 PHE 0.021 0.001 PHE Y 67 TYR 0.030 0.002 TYR C 207 ARG 0.003 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6992.02 seconds wall clock time: 121 minutes 51.97 seconds (7311.97 seconds total)