Starting phenix.real_space_refine on Fri Mar 15 21:47:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwt_35064/03_2024/8hwt_35064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwt_35064/03_2024/8hwt_35064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwt_35064/03_2024/8hwt_35064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwt_35064/03_2024/8hwt_35064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwt_35064/03_2024/8hwt_35064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwt_35064/03_2024/8hwt_35064.pdb" } resolution = 2.91 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 4775 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 32 5.16 5 C 5099 2.51 5 N 1346 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 46": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8077 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 189, 1515 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 189, 1515 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 1 bond proxies already assigned to first conformer: 1548 Chain: "H" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1617 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1632 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "D" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1662 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Time building chain proxies: 5.26, per 1000 atoms: 0.65 Number of scatterers: 8077 At special positions: 0 Unit cell: (68, 110.5, 123.25, 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 32 16.00 O 1600 8.00 N 1346 7.00 C 5099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 223 " - pdb=" SG CYS E 215 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.71 Conformation dependent library (CDL) restraints added in 1.7 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 10.6% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.613A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.738A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.370A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.926A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.990A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.843A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 removed outlier: 4.038A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.206A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.937A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.336A pdb=" N VAL H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.220A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 136 removed outlier: 5.220A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.741A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.741A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.139A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.702A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.269A pdb=" N ASP D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU D 45 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.850A pdb=" N CYS D 95 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP D 110 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG D 97 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AC2, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.692A pdb=" N LYS D 216 " --> pdb=" O CYS D 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.549A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.900A pdb=" N LEU E 11 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 115 through 119 Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 151 332 hydrogen bonds defined for protein. 815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2565 1.34 - 1.46: 2064 1.46 - 1.58: 3605 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8272 Sorted by residual: bond pdb=" N ALA E 113 " pdb=" CA ALA E 113 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.55e-02 4.16e+03 5.02e+00 bond pdb=" CA ALA E 113 " pdb=" CB ALA E 113 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.37e-02 5.33e+03 1.80e+00 bond pdb=" CA PRO E 114 " pdb=" C PRO E 114 " ideal model delta sigma weight residual 1.520 1.538 -0.018 1.42e-02 4.96e+03 1.62e+00 bond pdb=" C PRO E 114 " pdb=" O PRO E 114 " ideal model delta sigma weight residual 1.235 1.219 0.016 1.30e-02 5.92e+03 1.54e+00 bond pdb=" CB ASP L 94 " pdb=" CG ASP L 94 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 8267 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.14: 166 105.14 - 112.35: 4187 112.35 - 119.56: 2517 119.56 - 126.77: 4276 126.77 - 133.98: 109 Bond angle restraints: 11255 Sorted by residual: angle pdb=" N ALA E 113 " pdb=" CA ALA E 113 " pdb=" C ALA E 113 " ideal model delta sigma weight residual 110.31 115.85 -5.54 1.38e+00 5.25e-01 1.61e+01 angle pdb=" N PRO E 114 " pdb=" CA PRO E 114 " pdb=" C PRO E 114 " ideal model delta sigma weight residual 112.47 119.65 -7.18 2.06e+00 2.36e-01 1.22e+01 angle pdb=" C SER L 63 " pdb=" N GLY L 64 " pdb=" CA GLY L 64 " ideal model delta sigma weight residual 122.18 120.26 1.92 6.90e-01 2.10e+00 7.72e+00 angle pdb=" C ALA E 113 " pdb=" N PRO E 114 " pdb=" CA PRO E 114 " ideal model delta sigma weight residual 119.84 122.79 -2.95 1.25e+00 6.40e-01 5.55e+00 angle pdb=" C SER L 93 " pdb=" N ASP L 94 " pdb=" CA ASP L 94 " ideal model delta sigma weight residual 124.82 128.96 -4.14 1.78e+00 3.16e-01 5.42e+00 ... (remaining 11250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4532 17.28 - 34.56: 323 34.56 - 51.83: 56 51.83 - 69.11: 15 69.11 - 86.39: 11 Dihedral angle restraints: 4937 sinusoidal: 1872 harmonic: 3065 Sorted by residual: dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 127.41 -34.41 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CA ASN L 92 " pdb=" C ASN L 92 " pdb=" N SER L 93 " pdb=" CA SER L 93 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 930 0.044 - 0.088: 235 0.088 - 0.131: 85 0.131 - 0.175: 3 0.175 - 0.219: 1 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CA PRO E 114 " pdb=" N PRO E 114 " pdb=" C PRO E 114 " pdb=" CB PRO E 114 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP L 94 " pdb=" N ASP L 94 " pdb=" C ASP L 94 " pdb=" CB ASP L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB ILE A 358 " pdb=" CA ILE A 358 " pdb=" CG1 ILE A 358 " pdb=" CG2 ILE A 358 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1251 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " -0.039 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO H 153 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 188 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO H 189 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO L 40 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " 0.030 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1386 2.77 - 3.30: 6980 3.30 - 3.84: 12645 3.84 - 4.37: 14696 4.37 - 4.90: 26695 Nonbonded interactions: 62402 Sorted by model distance: nonbonded pdb=" O VAL D 128 " pdb=" NZ LYS D 216 " model vdw 2.241 2.520 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.259 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.272 2.440 nonbonded pdb=" OD2 ASP H 98 " pdb=" OH TYR L 96 " model vdw 2.273 2.440 nonbonded pdb=" NZ LYS E 39 " pdb=" O GLU E 81 " model vdw 2.287 2.520 ... (remaining 62397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid \ 55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ d 78 through 82 or resid 84 through 87 or resid 89 through 97 or resid 99 or res \ id 102 or resid 104 or resid 108 or resid 110 through 114 or resid 117 through 2 \ 22)) selection = (chain 'H' and (resid 2 through 11 or resid 13 through 26 or resid 30 through 31 \ or resid 34 or resid 36 through 39 or resid 42 through 49 or resid 51 or resid \ 55 or resid 57 or resid 59 or resid 61 through 71 or resid 75 through 76 or resi \ d 78 through 82 or resid 84 through 87 or resid 89 through 98 or resid 100 or re \ sid 102 or resid 105 or resid 107 through 111 or resid 114 through 219)) } ncs_group { reference = (chain 'E' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 13 or \ resid 15 through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 \ or resid 46 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 \ through 90 or resid 94 or resid 97 through 100 or resid 102 through 104 or resi \ d 107 through 214)) selection = (chain 'L' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 13 or \ resid 15 through 27 or resid 29 or resid 31 or resid 33 or resid 35 through 44 \ or resid 46 through 52 or resid 54 through 69 or resid 71 through 84 or resid 86 \ through 90 or resid 93 or resid 96 through 99 or resid 101 through 103 or resid \ 106 through 213)) } 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=0.45 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: 2.500 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: 0.000 Extract box with map and model: 9.700 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.690 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 0.003 0.047 8272 Z= 0.188 Angle : 0.559 8.022 11255 Z= 0.294 Chirality : 0.044 0.219 1254 Planarity : 0.005 0.060 1447 Dihedral : 12.838 86.391 2950 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.29 (0.26), residues: 1049 helix: -1.57 (0.70), residues: 50 sheet: 1.23 (0.25), residues: 433 loop : -0.47 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 36 HIS 0.002 0.001 HIS D 207 PHE 0.017 0.001 PHE A 515 TYR 0.015 0.001 TYR D 58 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8017 (t) cc_final: 0.7781 (p) REVERT: A 346 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.7011 (ttp-110) REVERT: A 472 ILE cc_start: 0.7927 (mm) cc_final: 0.7675 (mm) REVERT: H 109 GLN cc_start: 0.7322 (mm110) cc_final: 0.7020 (mm110) REVERT: L 3 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7307 (mm-40) REVERT: L 79 GLN cc_start: 0.8091 (mm110) cc_final: 0.7838 (mm110) REVERT: L 123 GLU cc_start: 0.8136 (mp0) cc_final: 0.7875 (mp0) REVERT: D 58 TYR cc_start: 0.7542 (m-10) cc_final: 0.7225 (m-80) REVERT: D 116 LEU cc_start: 0.6601 (tp) cc_final: 0.6342 (tt) REVERT: D 124 LYS cc_start: 0.7462 (tmtt) cc_final: 0.7246 (tmtm) REVERT: D 150 LYS cc_start: 0.7046 (tttm) cc_final: 0.6631 (tttm) REVERT: D 152 TYR cc_start: 0.7507 (p90) cc_final: 0.6866 (p90) REVERT: E 6 GLN cc_start: 0.6522 (mt0) cc_final: 0.6308 (mt0) REVERT: E 23 CYS cc_start: 0.5533 (t) cc_final: 0.4924 (t) REVERT: E 108 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7251 (ttpm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.9979 time to fit residues: 166.1428 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8272 Z= 0.186 Angle : 0.548 7.422 11255 Z= 0.277 Chirality : 0.043 0.163 1254 Planarity : 0.004 0.051 1447 Dihedral : 4.065 23.867 1153 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.76 % Allowed : 9.14 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.25 (0.26), residues: 1049 helix: -2.02 (0.61), residues: 57 sheet: 1.23 (0.25), residues: 450 loop : -0.50 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.002 0.001 HIS D 35 PHE 0.019 0.001 PHE H 67 TYR 0.015 0.001 TYR D 58 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8007 (t) cc_final: 0.7777 (p) REVERT: A 346 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.7008 (ttp-110) REVERT: A 472 ILE cc_start: 0.7963 (mm) cc_final: 0.7690 (mm) REVERT: H 109 GLN cc_start: 0.7314 (mm110) cc_final: 0.7005 (mm110) REVERT: L 3 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7291 (mm-40) REVERT: L 79 GLN cc_start: 0.8063 (mm110) cc_final: 0.7819 (mm110) REVERT: L 123 GLU cc_start: 0.8240 (mp0) cc_final: 0.7881 (mp0) REVERT: D 19 ARG cc_start: 0.7196 (ttm-80) cc_final: 0.6785 (ttm110) REVERT: D 58 TYR cc_start: 0.7232 (m-10) cc_final: 0.6672 (m-80) REVERT: D 82 MET cc_start: 0.7000 (mpt) cc_final: 0.6371 (mpt) REVERT: D 124 LYS cc_start: 0.7488 (tmtt) cc_final: 0.7265 (tmtm) REVERT: D 152 TYR cc_start: 0.7575 (p90) cc_final: 0.6980 (p90) REVERT: E 23 CYS cc_start: 0.5583 (t) cc_final: 0.5026 (t) REVERT: E 87 TYR cc_start: 0.7640 (m-80) cc_final: 0.7060 (m-80) REVERT: E 89 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7311 (tt0) REVERT: E 108 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7248 (ttpm) outliers start: 14 outliers final: 9 residues processed: 142 average time/residue: 0.9382 time to fit residues: 144.5690 Evaluate side-chains 144 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.0670 chunk 31 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 89 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8272 Z= 0.239 Angle : 0.551 6.893 11255 Z= 0.282 Chirality : 0.043 0.168 1254 Planarity : 0.004 0.049 1447 Dihedral : 4.142 23.795 1153 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.87 % Allowed : 11.01 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.25 (0.26), residues: 1049 helix: -2.01 (0.62), residues: 57 sheet: 1.19 (0.24), residues: 462 loop : -0.50 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.003 0.001 HIS D 35 PHE 0.014 0.001 PHE H 67 TYR 0.017 0.002 TYR D 106 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8023 (t) cc_final: 0.7788 (p) REVERT: A 346 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.7038 (ttp-110) REVERT: A 472 ILE cc_start: 0.7964 (mm) cc_final: 0.7701 (mm) REVERT: H 128 LEU cc_start: 0.7829 (mt) cc_final: 0.7601 (mp) REVERT: L 3 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7307 (mm-40) REVERT: L 79 GLN cc_start: 0.8080 (mm110) cc_final: 0.7829 (mm110) REVERT: L 123 GLU cc_start: 0.8264 (mp0) cc_final: 0.7895 (mp0) REVERT: D 20 LEU cc_start: 0.7192 (mp) cc_final: 0.6987 (mt) REVERT: D 58 TYR cc_start: 0.7390 (m-10) cc_final: 0.6851 (m-80) REVERT: D 124 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7293 (tmtp) REVERT: E 52 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7662 (p) REVERT: E 89 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7362 (tt0) REVERT: E 108 LYS cc_start: 0.7516 (ttpt) cc_final: 0.7252 (ttpm) outliers start: 15 outliers final: 12 residues processed: 140 average time/residue: 0.8970 time to fit residues: 135.9217 Evaluate side-chains 146 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 6 GLN L 89 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8272 Z= 0.271 Angle : 0.562 7.478 11255 Z= 0.287 Chirality : 0.044 0.166 1254 Planarity : 0.005 0.053 1447 Dihedral : 4.256 24.320 1153 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.08 % Allowed : 12.78 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.29 (0.26), residues: 1049 helix: -1.80 (0.67), residues: 51 sheet: 1.15 (0.24), residues: 462 loop : -0.44 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.003 0.001 HIS D 35 PHE 0.014 0.002 PHE L 116 TYR 0.016 0.002 TYR L 49 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8034 (t) cc_final: 0.7807 (p) REVERT: A 346 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.7037 (ttp-110) REVERT: A 472 ILE cc_start: 0.7975 (mm) cc_final: 0.7699 (mm) REVERT: L 3 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7303 (mm-40) REVERT: L 18 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7811 (ttm170) REVERT: L 79 GLN cc_start: 0.8095 (mm110) cc_final: 0.7820 (mm110) REVERT: L 91 LEU cc_start: 0.7579 (tm) cc_final: 0.7232 (mt) REVERT: L 123 GLU cc_start: 0.8217 (mp0) cc_final: 0.7845 (mp0) REVERT: D 20 LEU cc_start: 0.7170 (mp) cc_final: 0.6960 (mt) REVERT: D 58 TYR cc_start: 0.7421 (m-80) cc_final: 0.6814 (m-80) REVERT: D 124 LYS cc_start: 0.7751 (tmtt) cc_final: 0.7242 (tmtp) REVERT: E 52 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7707 (p) REVERT: E 89 GLN cc_start: 0.7779 (tt0) cc_final: 0.7513 (tt0) REVERT: E 108 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7301 (ttpm) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.8717 time to fit residues: 150.8511 Evaluate side-chains 173 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 144 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN L 166 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8272 Z= 0.314 Angle : 0.589 8.178 11255 Z= 0.300 Chirality : 0.045 0.167 1254 Planarity : 0.005 0.057 1447 Dihedral : 4.379 24.557 1153 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.52 % Allowed : 13.77 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.23 (0.26), residues: 1049 helix: -1.87 (0.67), residues: 51 sheet: 1.10 (0.24), residues: 463 loop : -0.48 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.004 0.001 HIS D 35 PHE 0.016 0.002 PHE L 116 TYR 0.018 0.002 TYR D 106 ARG 0.008 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8050 (t) cc_final: 0.7814 (p) REVERT: A 346 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.7058 (ttp-110) REVERT: A 472 ILE cc_start: 0.7974 (mm) cc_final: 0.7691 (mm) REVERT: L 3 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7321 (mm-40) REVERT: L 18 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7872 (ttm170) REVERT: L 79 GLN cc_start: 0.8104 (mm110) cc_final: 0.7809 (mm110) REVERT: L 91 LEU cc_start: 0.7607 (tm) cc_final: 0.7263 (mt) REVERT: L 123 GLU cc_start: 0.8251 (mp0) cc_final: 0.7877 (mp0) REVERT: D 20 LEU cc_start: 0.7272 (mp) cc_final: 0.7054 (mt) REVERT: D 58 TYR cc_start: 0.7513 (m-80) cc_final: 0.6838 (m-80) REVERT: D 124 LYS cc_start: 0.7758 (tmtt) cc_final: 0.7150 (tmtp) REVERT: E 4 MET cc_start: 0.7787 (mmm) cc_final: 0.7106 (mmm) REVERT: E 52 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7747 (p) REVERT: E 87 TYR cc_start: 0.7721 (m-80) cc_final: 0.7184 (m-80) REVERT: E 89 GLN cc_start: 0.7780 (tt0) cc_final: 0.7501 (tt0) REVERT: E 108 LYS cc_start: 0.7582 (ttpt) cc_final: 0.7307 (ttpm) outliers start: 30 outliers final: 22 residues processed: 167 average time/residue: 0.8817 time to fit residues: 159.3561 Evaluate side-chains 174 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN E 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8272 Z= 0.222 Angle : 0.556 7.961 11255 Z= 0.281 Chirality : 0.043 0.161 1254 Planarity : 0.005 0.058 1447 Dihedral : 4.232 24.046 1153 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.41 % Allowed : 14.76 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.19 (0.26), residues: 1049 helix: -2.07 (0.62), residues: 57 sheet: 1.09 (0.24), residues: 462 loop : -0.48 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.002 0.001 HIS D 35 PHE 0.011 0.001 PHE H 67 TYR 0.016 0.001 TYR D 106 ARG 0.009 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8047 (t) cc_final: 0.7832 (p) REVERT: A 346 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.7063 (ttp-110) REVERT: A 472 ILE cc_start: 0.7975 (mm) cc_final: 0.7691 (mm) REVERT: L 3 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7318 (mm-40) REVERT: L 18 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7851 (ttm170) REVERT: L 79 GLN cc_start: 0.8084 (mm110) cc_final: 0.7794 (mm110) REVERT: L 91 LEU cc_start: 0.7533 (tm) cc_final: 0.7181 (mt) REVERT: L 123 GLU cc_start: 0.8253 (mp0) cc_final: 0.7854 (mp0) REVERT: D 20 LEU cc_start: 0.7222 (mp) cc_final: 0.6996 (mt) REVERT: D 58 TYR cc_start: 0.7522 (m-80) cc_final: 0.6854 (m-80) REVERT: D 124 LYS cc_start: 0.7765 (tmtt) cc_final: 0.7225 (tmtp) REVERT: E 52 SER cc_start: 0.7886 (t) cc_final: 0.7661 (p) REVERT: E 87 TYR cc_start: 0.7664 (m-80) cc_final: 0.7142 (m-80) REVERT: E 89 GLN cc_start: 0.7730 (tt0) cc_final: 0.7507 (tt0) REVERT: E 108 LYS cc_start: 0.7590 (ttpt) cc_final: 0.7319 (ttpm) outliers start: 29 outliers final: 23 residues processed: 167 average time/residue: 0.8337 time to fit residues: 151.1489 Evaluate side-chains 179 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 165 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8272 Z= 0.289 Angle : 0.585 8.035 11255 Z= 0.296 Chirality : 0.044 0.167 1254 Planarity : 0.005 0.080 1447 Dihedral : 4.344 24.420 1153 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.63 % Allowed : 15.09 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.17 (0.26), residues: 1049 helix: -2.12 (0.61), residues: 57 sheet: 1.12 (0.24), residues: 461 loop : -0.53 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.003 0.001 HIS D 35 PHE 0.014 0.002 PHE L 116 TYR 0.017 0.002 TYR H 33 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8038 (t) cc_final: 0.7834 (p) REVERT: A 346 ARG cc_start: 0.7350 (ttp-110) cc_final: 0.7085 (ttp-110) REVERT: A 472 ILE cc_start: 0.7975 (mm) cc_final: 0.7689 (mm) REVERT: L 3 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7352 (mm-40) REVERT: L 18 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7901 (ttm170) REVERT: L 79 GLN cc_start: 0.8100 (mm110) cc_final: 0.7798 (mm110) REVERT: L 91 LEU cc_start: 0.7562 (tm) cc_final: 0.7217 (mt) REVERT: L 123 GLU cc_start: 0.8236 (mp0) cc_final: 0.7820 (mp0) REVERT: D 20 LEU cc_start: 0.7267 (mp) cc_final: 0.7018 (mt) REVERT: D 58 TYR cc_start: 0.7603 (m-80) cc_final: 0.6927 (m-80) REVERT: D 124 LYS cc_start: 0.7765 (tmtt) cc_final: 0.7254 (tmtp) REVERT: E 52 SER cc_start: 0.7944 (t) cc_final: 0.7723 (p) REVERT: E 87 TYR cc_start: 0.7715 (m-80) cc_final: 0.7173 (m-80) REVERT: E 89 GLN cc_start: 0.7775 (tt0) cc_final: 0.7401 (tt0) REVERT: E 108 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7341 (ttpm) outliers start: 31 outliers final: 26 residues processed: 165 average time/residue: 0.8015 time to fit residues: 143.8380 Evaluate side-chains 179 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8272 Z= 0.297 Angle : 0.585 8.234 11255 Z= 0.298 Chirality : 0.044 0.162 1254 Planarity : 0.005 0.068 1447 Dihedral : 4.402 24.984 1153 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.63 % Allowed : 15.64 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.23 (0.26), residues: 1049 helix: -1.84 (0.67), residues: 51 sheet: 1.12 (0.24), residues: 461 loop : -0.50 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.003 0.001 HIS D 35 PHE 0.024 0.002 PHE H 67 TYR 0.018 0.002 TYR H 33 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8044 (t) cc_final: 0.7838 (p) REVERT: A 346 ARG cc_start: 0.7360 (ttp-110) cc_final: 0.7097 (ttp-110) REVERT: A 472 ILE cc_start: 0.7975 (mm) cc_final: 0.7687 (mm) REVERT: L 3 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7359 (mm-40) REVERT: L 18 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7936 (ttm170) REVERT: L 79 GLN cc_start: 0.8141 (mm110) cc_final: 0.7836 (mm110) REVERT: L 91 LEU cc_start: 0.7576 (tm) cc_final: 0.7233 (mt) REVERT: L 123 GLU cc_start: 0.8240 (mp0) cc_final: 0.7826 (mp0) REVERT: D 20 LEU cc_start: 0.7238 (mp) cc_final: 0.6982 (mt) REVERT: D 58 TYR cc_start: 0.7651 (m-80) cc_final: 0.7052 (m-80) REVERT: D 124 LYS cc_start: 0.7731 (tmtt) cc_final: 0.7252 (tmtp) REVERT: E 52 SER cc_start: 0.7932 (OUTLIER) cc_final: 0.7718 (p) REVERT: E 87 TYR cc_start: 0.7707 (m-80) cc_final: 0.7159 (m-80) REVERT: E 89 GLN cc_start: 0.7741 (tt0) cc_final: 0.7369 (tt0) REVERT: E 108 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7327 (ttpm) outliers start: 31 outliers final: 25 residues processed: 160 average time/residue: 0.7956 time to fit residues: 138.2708 Evaluate side-chains 176 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E 6 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8272 Z= 0.258 Angle : 0.578 8.444 11255 Z= 0.291 Chirality : 0.044 0.165 1254 Planarity : 0.005 0.064 1447 Dihedral : 4.340 24.136 1153 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.41 % Allowed : 15.75 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.18 (0.26), residues: 1049 helix: -2.05 (0.59), residues: 63 sheet: 1.16 (0.24), residues: 458 loop : -0.53 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 47 HIS 0.003 0.001 HIS D 35 PHE 0.023 0.002 PHE H 67 TYR 0.017 0.002 TYR L 96 ARG 0.011 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 345 THR cc_start: 0.8058 (t) cc_final: 0.7853 (p) REVERT: A 346 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7115 (ttp-110) REVERT: A 472 ILE cc_start: 0.7979 (mm) cc_final: 0.7684 (mm) REVERT: L 3 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7358 (mm-40) REVERT: L 18 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7932 (ttm170) REVERT: L 79 GLN cc_start: 0.8131 (mm110) cc_final: 0.7825 (mm110) REVERT: L 91 LEU cc_start: 0.7533 (tm) cc_final: 0.7307 (tt) REVERT: L 123 GLU cc_start: 0.8231 (mp0) cc_final: 0.7818 (mp0) REVERT: D 20 LEU cc_start: 0.7154 (mp) cc_final: 0.6903 (mt) REVERT: D 58 TYR cc_start: 0.7656 (m-80) cc_final: 0.7042 (m-80) REVERT: D 124 LYS cc_start: 0.7766 (tmtt) cc_final: 0.7288 (tmtp) REVERT: D 148 LEU cc_start: 0.7114 (tp) cc_final: 0.6827 (tm) REVERT: E 52 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7699 (p) REVERT: E 87 TYR cc_start: 0.7679 (m-80) cc_final: 0.7131 (m-80) REVERT: E 89 GLN cc_start: 0.7714 (tt0) cc_final: 0.7484 (tt0) REVERT: E 108 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7352 (ttpm) outliers start: 29 outliers final: 25 residues processed: 161 average time/residue: 0.8202 time to fit residues: 143.3835 Evaluate side-chains 179 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 0.0020 chunk 81 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 0.0070 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN E 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8272 Z= 0.170 Angle : 0.537 8.189 11255 Z= 0.269 Chirality : 0.043 0.156 1254 Planarity : 0.005 0.060 1447 Dihedral : 4.097 23.457 1153 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.64 % Allowed : 16.74 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.31 (0.26), residues: 1049 helix: -1.96 (0.59), residues: 63 sheet: 1.21 (0.24), residues: 459 loop : -0.41 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS D 35 PHE 0.021 0.001 PHE A 374 TYR 0.017 0.001 TYR D 106 ARG 0.011 0.000 ARG E 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7122 (ttp-110) REVERT: A 472 ILE cc_start: 0.7971 (mm) cc_final: 0.7666 (mm) REVERT: L 3 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7327 (mm-40) REVERT: L 18 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7849 (ttm170) REVERT: L 52 SER cc_start: 0.8284 (t) cc_final: 0.8070 (m) REVERT: L 79 GLN cc_start: 0.8113 (mm110) cc_final: 0.7835 (mm110) REVERT: L 123 GLU cc_start: 0.8241 (mp0) cc_final: 0.7843 (mp0) REVERT: D 20 LEU cc_start: 0.7152 (mp) cc_final: 0.6923 (mt) REVERT: D 58 TYR cc_start: 0.7611 (m-80) cc_final: 0.6973 (m-80) REVERT: D 124 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7306 (tmtp) REVERT: E 52 SER cc_start: 0.7792 (t) cc_final: 0.7587 (p) REVERT: E 108 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7387 (ttpm) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.8696 time to fit residues: 149.7931 Evaluate side-chains 165 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 4 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 89 GLN E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116376 restraints weight = 14502.008| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.90 r_work: 0.3430 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8272 Z= 0.183 Angle : 0.555 8.645 11255 Z= 0.274 Chirality : 0.043 0.163 1254 Planarity : 0.005 0.060 1447 Dihedral : 4.065 23.735 1153 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.64 % Allowed : 17.07 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.36 (0.26), residues: 1049 helix: -1.96 (0.59), residues: 63 sheet: 1.27 (0.24), residues: 457 loop : -0.40 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 36 HIS 0.002 0.001 HIS D 35 PHE 0.025 0.001 PHE A 374 TYR 0.016 0.001 TYR D 106 ARG 0.012 0.000 ARG E 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.32 seconds wall clock time: 57 minutes 50.86 seconds (3470.86 seconds total)