Starting phenix.real_space_refine on Sat Jul 26 06:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7la4_23245/07_2025/7la4_23245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7la4_23245/07_2025/7la4_23245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2025/7la4_23245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2025/7la4_23245.map" model { file = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2025/7la4_23245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2025/7la4_23245.cif" } resolution = 3.3 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 33 5.16 5 C 5213 2.51 5 N 1386 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8281 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3467 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 27, 'TRANS': 424} Chain: "B" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2940 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 357} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.67, per 1000 atoms: 0.68 Number of scatterers: 8281 At special positions: 0 Unit cell: (102, 110, 100, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 33 16.00 Mg 1 11.99 O 1642 8.00 N 1386 7.00 C 5213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " 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 Links applied ALPHA1-3 " MAN D 3 " - " MAN D 4 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1105 " - " ASN A 15 " " NAG C 1 " - " ASN B 99 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN B 371 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 11.6% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.940A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.605A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.575A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.058A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.760A pdb=" N ARG B 202 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.889A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.794A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.865A pdb=" N LYS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.775A pdb=" N ASN B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.916A pdb=" N VAL B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.733A pdb=" N GLN L 89 " --> pdb=" O ASN L 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.551A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.502A pdb=" N PHE A 87 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.738A pdb=" N GLU A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AB2, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.569A pdb=" N GLU A 252 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 256 through 257 removed outlier: 6.323A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 293 through 295 removed outlier: 3.535A pdb=" N VAL A 308 " --> pdb=" O TYR A 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AB6, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.691A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 102 removed outlier: 3.784A pdb=" N LYS B 98 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 401 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 102 removed outlier: 3.784A pdb=" N LYS B 98 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 401 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 197 removed outlier: 4.655A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 112 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY B 152 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 114 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY B 154 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 116 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE B 156 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 118 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 247 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 432 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: 2.37 Time building geometry restraints manager: 2.92 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: 2701 1.34 - 1.46: 1858 1.46 - 1.58: 3847 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 8455 Sorted by residual: bond pdb=" N ILE H 72 " pdb=" CA ILE H 72 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.07e-02 8.73e+03 1.03e+01 bond pdb=" N TYR H 100 " pdb=" CA TYR H 100 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.59e+00 bond pdb=" N ILE L 106 " pdb=" CA ILE L 106 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N ARG L 24 " pdb=" CA ARG L 24 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.08e+00 ... (remaining 8450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10666 1.49 - 2.98: 677 2.98 - 4.46: 108 4.46 - 5.95: 23 5.95 - 7.44: 12 Bond angle restraints: 11486 Sorted by residual: angle pdb=" N PHE H 104 " pdb=" CA PHE H 104 " pdb=" C PHE H 104 " ideal model delta sigma weight residual 111.71 105.39 6.32 1.34e+00 5.57e-01 2.23e+01 angle pdb=" N ASN L 31 " pdb=" CA ASN L 31 " pdb=" C ASN L 31 " ideal model delta sigma weight residual 112.30 106.45 5.85 1.36e+00 5.41e-01 1.85e+01 angle pdb=" N VAL B 314 " pdb=" CA VAL B 314 " pdb=" C VAL B 314 " ideal model delta sigma weight residual 113.20 109.15 4.05 9.60e-01 1.09e+00 1.78e+01 angle pdb=" N MET H 81 " pdb=" CA MET H 81 " pdb=" C MET H 81 " ideal model delta sigma weight residual 114.64 108.32 6.32 1.52e+00 4.33e-01 1.73e+01 angle pdb=" CA ARG H 84 " pdb=" C ARG H 84 " pdb=" O ARG H 84 " ideal model delta sigma weight residual 121.60 116.89 4.71 1.21e+00 6.83e-01 1.52e+01 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 4827 24.14 - 48.28: 262 48.28 - 72.41: 47 72.41 - 96.55: 20 96.55 - 120.69: 4 Dihedral angle restraints: 5160 sinusoidal: 2151 harmonic: 3009 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 45.51 47.49 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA ASN B 377 " pdb=" C ASN B 377 " pdb=" N GLU B 378 " pdb=" CA GLU B 378 " ideal model delta harmonic sigma weight residual -180.00 -152.33 -27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA THR H 28 " pdb=" C THR H 28 " pdb=" N PHE H 29 " pdb=" CA PHE H 29 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1242 0.113 - 0.225: 44 0.225 - 0.338: 5 0.338 - 0.450: 0 0.450 - 0.563: 1 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CA TYR H 106 " pdb=" N TYR H 106 " pdb=" C TYR H 106 " pdb=" CB TYR H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LEU A 84 " pdb=" N LEU A 84 " pdb=" C LEU A 84 " pdb=" CB LEU A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1289 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 288 " -0.026 2.00e-02 2.50e+03 1.85e-02 6.81e+00 pdb=" CG TYR A 288 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 288 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 288 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 288 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 288 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 288 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 288 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 99 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.25e+00 pdb=" CG ASN B 99 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 99 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 99 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.013 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP H 47 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.001 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 244 2.66 - 3.22: 8204 3.22 - 3.78: 13004 3.78 - 4.34: 18660 4.34 - 4.90: 30829 Nonbonded interactions: 70941 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B2001 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASN A 430 " pdb=" O HOH A1201 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 353 " pdb=" OE1 GLU B 297 " model vdw 2.138 3.040 nonbonded pdb=" OG SER A 22 " pdb=" O GLY A 94 " model vdw 2.156 3.040 nonbonded pdb=" OE1 GLN A 197 " pdb=" OG SER A 220 " model vdw 2.159 3.040 ... (remaining 70936 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.490 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.006 0.046 8473 Z= 0.320 Angle : 0.853 7.438 11532 Z= 0.493 Chirality : 0.056 0.563 1292 Planarity : 0.004 0.043 1485 Dihedral : 16.129 120.689 3224 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.58 % Favored : 89.94 % Rotamer: Outliers : 1.91 % Allowed : 2.70 % Favored : 95.39 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.55 % 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: -4.02 (0.24), residues: 1044 helix: -3.78 (0.40), residues: 95 sheet: -2.97 (0.25), residues: 351 loop : -2.26 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 47 HIS 0.010 0.001 HIS A 278 PHE 0.017 0.002 PHE B 370 TYR 0.044 0.002 TYR A 288 ARG 0.010 0.001 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 4) link_NAG-ASN : angle 2.90592 ( 12) link_ALPHA1-4 : bond 0.01025 ( 2) link_ALPHA1-4 : angle 2.77565 ( 6) link_BETA1-4 : bond 0.00639 ( 3) link_BETA1-4 : angle 1.64593 ( 9) link_ALPHA1-3 : bond 0.01013 ( 1) link_ALPHA1-3 : angle 1.67376 ( 3) hydrogen bonds : bond 0.25976 ( 178) hydrogen bonds : angle 11.85270 ( 432) SS BOND : bond 0.00457 ( 8) SS BOND : angle 1.23502 ( 16) covalent geometry : bond 0.00597 ( 8455) covalent geometry : angle 0.84387 (11486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 26 SER cc_start: 0.7800 (p) cc_final: 0.7471 (t) REVERT: A 232 ASP cc_start: 0.8233 (m-30) cc_final: 0.7992 (m-30) outliers start: 17 outliers final: 2 residues processed: 158 average time/residue: 0.2274 time to fit residues: 48.9221 Evaluate side-chains 121 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 72 LEU 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: 0.0030 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114910 restraints weight = 11449.995| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.84 r_work: 0.3282 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8473 Z= 0.146 Angle : 0.680 7.384 11532 Z= 0.342 Chirality : 0.048 0.390 1292 Planarity : 0.004 0.048 1485 Dihedral : 10.565 106.201 1355 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.48 % Favored : 90.33 % Rotamer: Outliers : 2.13 % Allowed : 10.00 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.77 (0.24), residues: 1044 helix: -3.47 (0.37), residues: 98 sheet: -2.99 (0.24), residues: 353 loop : -1.95 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 235 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.001 PHE A 87 TYR 0.027 0.002 TYR A 288 ARG 0.006 0.001 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 4) link_NAG-ASN : angle 2.48608 ( 12) link_ALPHA1-4 : bond 0.02028 ( 2) link_ALPHA1-4 : angle 3.76249 ( 6) link_BETA1-4 : bond 0.00423 ( 3) link_BETA1-4 : angle 1.36521 ( 9) link_ALPHA1-3 : bond 0.02282 ( 1) link_ALPHA1-3 : angle 3.25317 ( 3) hydrogen bonds : bond 0.04413 ( 178) hydrogen bonds : angle 8.38181 ( 432) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.93971 ( 16) covalent geometry : bond 0.00323 ( 8455) covalent geometry : angle 0.66714 (11486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: A 285 MET cc_start: 0.8913 (mtp) cc_final: 0.8630 (mtm) REVERT: B 390 LYS cc_start: 0.6751 (tmtt) cc_final: 0.6334 (mttm) outliers start: 19 outliers final: 8 residues processed: 154 average time/residue: 0.3306 time to fit residues: 74.5574 Evaluate side-chains 136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.0020 chunk 97 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 27 GLN L 38 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111972 restraints weight = 11332.153| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.23 r_work: 0.3252 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8473 Z= 0.134 Angle : 0.648 10.736 11532 Z= 0.320 Chirality : 0.045 0.185 1292 Planarity : 0.004 0.049 1485 Dihedral : 9.912 105.834 1353 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.14 % Favored : 91.76 % Rotamer: Outliers : 1.57 % Allowed : 14.83 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.39 (0.24), residues: 1044 helix: -3.01 (0.41), residues: 91 sheet: -2.61 (0.25), residues: 356 loop : -1.84 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 235 HIS 0.006 0.001 HIS A 338 PHE 0.020 0.001 PHE B 100 TYR 0.023 0.002 TYR A 288 ARG 0.005 0.001 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 4) link_NAG-ASN : angle 3.92128 ( 12) link_ALPHA1-4 : bond 0.02033 ( 2) link_ALPHA1-4 : angle 3.74501 ( 6) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 1.05768 ( 9) link_ALPHA1-3 : bond 0.02230 ( 1) link_ALPHA1-3 : angle 3.37160 ( 3) hydrogen bonds : bond 0.03577 ( 178) hydrogen bonds : angle 7.52042 ( 432) SS BOND : bond 0.00276 ( 8) SS BOND : angle 0.77821 ( 16) covalent geometry : bond 0.00298 ( 8455) covalent geometry : angle 0.62705 (11486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8602 (tm-30) REVERT: H 23 LYS cc_start: 0.8328 (tppt) cc_final: 0.7745 (tptp) REVERT: L 61 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7824 (mtm-85) REVERT: L 79 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 208 ARG cc_start: 0.8351 (mmt-90) cc_final: 0.8024 (mmt-90) REVERT: B 390 LYS cc_start: 0.6674 (tmtt) cc_final: 0.6145 (mttm) outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.2920 time to fit residues: 57.6868 Evaluate side-chains 133 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110236 restraints weight = 11340.936| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.22 r_work: 0.3228 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8473 Z= 0.171 Angle : 0.684 12.513 11532 Z= 0.330 Chirality : 0.048 0.403 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.660 103.842 1351 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.70 % Allowed : 15.96 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.33 (0.25), residues: 1044 helix: -2.90 (0.41), residues: 91 sheet: -2.66 (0.25), residues: 363 loop : -1.72 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 107 HIS 0.007 0.001 HIS A 338 PHE 0.017 0.002 PHE B 100 TYR 0.024 0.002 TYR A 288 ARG 0.006 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 4) link_NAG-ASN : angle 5.10778 ( 12) link_ALPHA1-4 : bond 0.02108 ( 2) link_ALPHA1-4 : angle 3.75520 ( 6) link_BETA1-4 : bond 0.00900 ( 3) link_BETA1-4 : angle 1.60473 ( 9) link_ALPHA1-3 : bond 0.02015 ( 1) link_ALPHA1-3 : angle 3.30546 ( 3) hydrogen bonds : bond 0.03287 ( 178) hydrogen bonds : angle 7.31683 ( 432) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.73930 ( 16) covalent geometry : bond 0.00392 ( 8455) covalent geometry : angle 0.65492 (11486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8610 (tm-30) REVERT: H 23 LYS cc_start: 0.8330 (tppt) cc_final: 0.7746 (tptp) REVERT: H 69 THR cc_start: 0.8161 (m) cc_final: 0.7913 (p) REVERT: L 6 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: L 39 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8341 (mttt) REVERT: L 79 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 208 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8002 (mmt-90) REVERT: A 285 MET cc_start: 0.8869 (mtm) cc_final: 0.8576 (mtm) REVERT: B 390 LYS cc_start: 0.6590 (tmtt) cc_final: 0.6089 (mttm) outliers start: 24 outliers final: 18 residues processed: 144 average time/residue: 0.2624 time to fit residues: 51.6811 Evaluate side-chains 146 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 227 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109420 restraints weight = 11189.426| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.21 r_work: 0.3216 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8473 Z= 0.187 Angle : 0.664 10.280 11532 Z= 0.325 Chirality : 0.046 0.194 1292 Planarity : 0.004 0.045 1485 Dihedral : 9.441 102.974 1351 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.71 % Allowed : 16.40 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.27 (0.25), residues: 1044 helix: -2.81 (0.41), residues: 91 sheet: -2.60 (0.25), residues: 367 loop : -1.69 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.002 PHE A 171 TYR 0.024 0.002 TYR A 288 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 4) link_NAG-ASN : angle 3.94742 ( 12) link_ALPHA1-4 : bond 0.02198 ( 2) link_ALPHA1-4 : angle 3.80885 ( 6) link_BETA1-4 : bond 0.00465 ( 3) link_BETA1-4 : angle 0.96745 ( 9) link_ALPHA1-3 : bond 0.02233 ( 1) link_ALPHA1-3 : angle 3.45111 ( 3) hydrogen bonds : bond 0.03204 ( 178) hydrogen bonds : angle 7.17704 ( 432) SS BOND : bond 0.00337 ( 8) SS BOND : angle 0.78190 ( 16) covalent geometry : bond 0.00433 ( 8455) covalent geometry : angle 0.64308 (11486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8576 (tm-30) REVERT: H 10 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8189 (mm-30) REVERT: H 23 LYS cc_start: 0.8340 (tppt) cc_final: 0.7775 (tptp) REVERT: H 69 THR cc_start: 0.8229 (m) cc_final: 0.8018 (p) REVERT: L 79 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 157 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7764 (tm-30) REVERT: A 208 ARG cc_start: 0.8365 (mmt-90) cc_final: 0.8004 (mmt-90) REVERT: A 285 MET cc_start: 0.8919 (mtm) cc_final: 0.8635 (mtm) REVERT: B 124 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7959 (mmt) REVERT: B 390 LYS cc_start: 0.6617 (tmtt) cc_final: 0.6119 (mttm) REVERT: B 400 GLU cc_start: 0.7869 (tt0) cc_final: 0.7470 (mm-30) outliers start: 33 outliers final: 24 residues processed: 148 average time/residue: 0.2659 time to fit residues: 55.5580 Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109442 restraints weight = 11314.255| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.22 r_work: 0.3219 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8473 Z= 0.176 Angle : 0.660 8.377 11532 Z= 0.323 Chirality : 0.046 0.216 1292 Planarity : 0.004 0.044 1485 Dihedral : 11.019 120.560 1351 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.60 % Allowed : 16.74 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.21 (0.25), residues: 1044 helix: -2.74 (0.42), residues: 91 sheet: -2.53 (0.25), residues: 372 loop : -1.66 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.014 0.002 PHE B 100 TYR 0.021 0.002 TYR A 288 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 4) link_NAG-ASN : angle 2.27822 ( 12) link_ALPHA1-4 : bond 0.02292 ( 2) link_ALPHA1-4 : angle 4.03400 ( 6) link_BETA1-4 : bond 0.00554 ( 3) link_BETA1-4 : angle 1.37053 ( 9) link_ALPHA1-3 : bond 0.02313 ( 1) link_ALPHA1-3 : angle 3.55226 ( 3) hydrogen bonds : bond 0.03137 ( 178) hydrogen bonds : angle 7.12469 ( 432) SS BOND : bond 0.00310 ( 8) SS BOND : angle 0.72930 ( 16) covalent geometry : bond 0.00405 ( 8455) covalent geometry : angle 0.64618 (11486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8562 (tt0) REVERT: H 47 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7692 (t60) REVERT: L 39 LYS cc_start: 0.8549 (mttt) cc_final: 0.8309 (mttt) REVERT: L 79 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 157 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7734 (tm-30) REVERT: A 208 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.7981 (mmt-90) REVERT: A 285 MET cc_start: 0.8949 (mtm) cc_final: 0.8747 (mtm) REVERT: B 124 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7865 (mmt) REVERT: B 390 LYS cc_start: 0.6596 (tmtt) cc_final: 0.6086 (mttm) REVERT: B 400 GLU cc_start: 0.7820 (tt0) cc_final: 0.7430 (mm-30) outliers start: 32 outliers final: 25 residues processed: 150 average time/residue: 0.2518 time to fit residues: 51.9152 Evaluate side-chains 149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110035 restraints weight = 11340.401| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.13 r_work: 0.3232 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8473 Z= 0.175 Angle : 0.693 13.002 11532 Z= 0.330 Chirality : 0.047 0.372 1292 Planarity : 0.004 0.043 1485 Dihedral : 9.543 101.555 1351 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.60 % Allowed : 17.75 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.14 (0.25), residues: 1044 helix: -2.63 (0.41), residues: 91 sheet: -2.46 (0.25), residues: 372 loop : -1.64 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.012 0.001 PHE A 171 TYR 0.022 0.002 TYR A 288 ARG 0.006 0.000 ARG H 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 4) link_NAG-ASN : angle 5.11622 ( 12) link_ALPHA1-4 : bond 0.02431 ( 2) link_ALPHA1-4 : angle 4.13961 ( 6) link_BETA1-4 : bond 0.01201 ( 3) link_BETA1-4 : angle 1.58390 ( 9) link_ALPHA1-3 : bond 0.02336 ( 1) link_ALPHA1-3 : angle 3.64591 ( 3) hydrogen bonds : bond 0.03114 ( 178) hydrogen bonds : angle 6.98226 ( 432) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.76868 ( 16) covalent geometry : bond 0.00400 ( 8455) covalent geometry : angle 0.66267 (11486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.7672 (t60) REVERT: L 39 LYS cc_start: 0.8610 (mttt) cc_final: 0.8401 (mttt) REVERT: L 79 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 157 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7746 (tm-30) REVERT: A 208 ARG cc_start: 0.8398 (mmt-90) cc_final: 0.8030 (mmt-90) REVERT: B 124 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7915 (mmt) REVERT: B 149 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8224 (pt) REVERT: B 390 LYS cc_start: 0.6640 (tmtt) cc_final: 0.6166 (mttm) outliers start: 32 outliers final: 25 residues processed: 148 average time/residue: 0.2316 time to fit residues: 47.6951 Evaluate side-chains 150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 403 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.0270 chunk 69 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108881 restraints weight = 11505.205| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.26 r_work: 0.3187 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8473 Z= 0.204 Angle : 0.686 8.680 11532 Z= 0.335 Chirality : 0.046 0.180 1292 Planarity : 0.004 0.043 1485 Dihedral : 10.523 114.065 1351 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.82 % Allowed : 18.20 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.17 (0.25), residues: 1044 helix: -2.58 (0.41), residues: 91 sheet: -2.50 (0.25), residues: 373 loop : -1.67 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.002 PHE A 171 TYR 0.023 0.002 TYR A 288 ARG 0.004 0.000 ARG H 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 4) link_NAG-ASN : angle 3.10678 ( 12) link_ALPHA1-4 : bond 0.02397 ( 2) link_ALPHA1-4 : angle 4.08928 ( 6) link_BETA1-4 : bond 0.00489 ( 3) link_BETA1-4 : angle 1.37985 ( 9) link_ALPHA1-3 : bond 0.02521 ( 1) link_ALPHA1-3 : angle 3.71504 ( 3) hydrogen bonds : bond 0.03167 ( 178) hydrogen bonds : angle 7.07118 ( 432) SS BOND : bond 0.00360 ( 8) SS BOND : angle 0.82594 ( 16) covalent geometry : bond 0.00473 ( 8455) covalent geometry : angle 0.66933 (11486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8605 (tpp) cc_final: 0.8327 (mmm) REVERT: H 47 TRP cc_start: 0.8031 (OUTLIER) cc_final: 0.7646 (t60) REVERT: L 79 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8049 (mt-10) REVERT: A 157 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7746 (tm-30) REVERT: A 208 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.8020 (mmt-90) REVERT: B 124 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7855 (mmt) REVERT: B 149 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (pt) REVERT: B 390 LYS cc_start: 0.6542 (tmtt) cc_final: 0.6067 (mttm) REVERT: B 400 GLU cc_start: 0.7827 (tt0) cc_final: 0.7396 (mm-30) outliers start: 34 outliers final: 27 residues processed: 141 average time/residue: 0.2412 time to fit residues: 48.1437 Evaluate side-chains 150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 77 optimal weight: 0.0060 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111377 restraints weight = 11446.832| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.26 r_work: 0.3232 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8473 Z= 0.147 Angle : 0.680 11.974 11532 Z= 0.325 Chirality : 0.047 0.402 1292 Planarity : 0.004 0.045 1485 Dihedral : 8.704 100.388 1351 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.15 % Allowed : 19.10 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -2.98 (0.25), residues: 1044 helix: -2.31 (0.44), residues: 88 sheet: -2.37 (0.26), residues: 349 loop : -1.64 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 PHE 0.013 0.001 PHE B 100 TYR 0.019 0.001 TYR A 288 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 5.14735 ( 12) link_ALPHA1-4 : bond 0.02544 ( 2) link_ALPHA1-4 : angle 4.23616 ( 6) link_BETA1-4 : bond 0.00873 ( 3) link_BETA1-4 : angle 0.84415 ( 9) link_ALPHA1-3 : bond 0.02451 ( 1) link_ALPHA1-3 : angle 3.82474 ( 3) hydrogen bonds : bond 0.02994 ( 178) hydrogen bonds : angle 6.85646 ( 432) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.70688 ( 16) covalent geometry : bond 0.00332 ( 8455) covalent geometry : angle 0.65018 (11486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7605 (t60) REVERT: L 79 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 157 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7714 (tm-30) REVERT: A 208 ARG cc_start: 0.8355 (mmt-90) cc_final: 0.8003 (mmt-90) REVERT: A 285 MET cc_start: 0.8927 (mtm) cc_final: 0.8668 (ttm) REVERT: B 124 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7846 (mmt) REVERT: B 390 LYS cc_start: 0.6666 (tmtt) cc_final: 0.6179 (mttm) outliers start: 28 outliers final: 21 residues processed: 139 average time/residue: 0.2266 time to fit residues: 43.9287 Evaluate side-chains 148 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 0.1980 chunk 98 optimal weight: 0.0970 chunk 67 optimal weight: 0.0370 chunk 49 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113889 restraints weight = 11271.159| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.25 r_work: 0.3266 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8473 Z= 0.120 Angle : 0.654 9.276 11532 Z= 0.317 Chirality : 0.045 0.220 1292 Planarity : 0.004 0.047 1485 Dihedral : 9.990 116.744 1351 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.58 % Allowed : 19.78 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.86 (0.25), residues: 1044 helix: -2.08 (0.45), residues: 88 sheet: -2.25 (0.27), residues: 337 loop : -1.63 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 235 HIS 0.005 0.001 HIS A 338 PHE 0.009 0.001 PHE B 100 TYR 0.013 0.001 TYR A 288 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 4) link_NAG-ASN : angle 2.87551 ( 12) link_ALPHA1-4 : bond 0.02610 ( 2) link_ALPHA1-4 : angle 4.33649 ( 6) link_BETA1-4 : bond 0.00637 ( 3) link_BETA1-4 : angle 1.33974 ( 9) link_ALPHA1-3 : bond 0.02524 ( 1) link_ALPHA1-3 : angle 3.98521 ( 3) hydrogen bonds : bond 0.02958 ( 178) hydrogen bonds : angle 6.79583 ( 432) SS BOND : bond 0.00189 ( 8) SS BOND : angle 0.58571 ( 16) covalent geometry : bond 0.00259 ( 8455) covalent geometry : angle 0.63583 (11486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: H 47 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.7580 (t60) REVERT: L 79 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 259 THR cc_start: 0.9005 (m) cc_final: 0.8643 (p) REVERT: A 285 MET cc_start: 0.8898 (mtm) cc_final: 0.8675 (ttm) REVERT: B 124 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7773 (mmt) REVERT: B 343 LEU cc_start: 0.8546 (tt) cc_final: 0.8279 (tt) REVERT: B 390 LYS cc_start: 0.6652 (tmtt) cc_final: 0.6226 (mttm) REVERT: B 400 GLU cc_start: 0.7800 (tt0) cc_final: 0.7313 (mm-30) outliers start: 23 outliers final: 18 residues processed: 142 average time/residue: 0.2763 time to fit residues: 57.1784 Evaluate side-chains 142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 86 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112101 restraints weight = 11475.268| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.26 r_work: 0.3252 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8473 Z= 0.156 Angle : 0.682 12.919 11532 Z= 0.323 Chirality : 0.046 0.354 1292 Planarity : 0.004 0.047 1485 Dihedral : 8.009 98.549 1351 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.36 % Allowed : 20.56 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -2.77 (0.25), residues: 1044 helix: -1.94 (0.46), residues: 88 sheet: -2.17 (0.27), residues: 337 loop : -1.59 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 PHE 0.019 0.001 PHE B 100 TYR 0.017 0.001 TYR A 288 ARG 0.003 0.000 ARG H 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 4) link_NAG-ASN : angle 5.34046 ( 12) link_ALPHA1-4 : bond 0.02730 ( 2) link_ALPHA1-4 : angle 4.50758 ( 6) link_BETA1-4 : bond 0.00838 ( 3) link_BETA1-4 : angle 0.65707 ( 9) link_ALPHA1-3 : bond 0.02520 ( 1) link_ALPHA1-3 : angle 3.97931 ( 3) hydrogen bonds : bond 0.02915 ( 178) hydrogen bonds : angle 6.73158 ( 432) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.77474 ( 16) covalent geometry : bond 0.00356 ( 8455) covalent geometry : angle 0.64865 (11486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6055.80 seconds wall clock time: 112 minutes 20.42 seconds (6740.42 seconds total)