Starting phenix.real_space_refine on Wed Mar 12 23:50:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7la4_23245/03_2025/7la4_23245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7la4_23245/03_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_23245/03_2025/7la4_23245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_2025/7la4_23245.map" model { file = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_2025/7la4_23245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_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-5624/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: 7.36, per 1000 atoms: 0.89 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: 3.05 Conformation dependent library (CDL) restraints added in 1.2 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: 1.16 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: 2.64 Time building geometry restraints manager: 3.50 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: 3.140 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.700 Find NCS groups from input model: 0.110 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- 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 8455 Z= 0.393 Angle : 0.844 7.438 11486 Z= 0.492 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 *********************** 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 : 0.971 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: 0.2334 time to fit residues: 50.1718 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 : 0.953 ------------------------------------------------------------------------------- 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: 0.0370 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: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115055 restraints weight = 11448.286| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.82 r_work: 0.3277 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8455 Z= 0.211 Angle : 0.670 7.425 11486 Z= 0.341 Chirality : 0.048 0.377 1292 Planarity : 0.004 0.047 1485 Dihedral : 10.569 106.103 1355 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.48 % Favored : 90.33 % Rotamer: Outliers : 2.13 % Allowed : 10.11 % Favored : 87.75 % 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: -3.77 (0.24), residues: 1044 helix: -3.48 (0.37), residues: 98 sheet: -3.00 (0.24), residues: 353 loop : -1.95 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 235 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.001 PHE B 308 TYR 0.025 0.002 TYR A 288 ARG 0.005 0.001 ARG A 41 *********************** 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 : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.8005 (mtm-85) REVERT: A 285 MET cc_start: 0.8928 (mtp) cc_final: 0.8651 (mtm) REVERT: B 390 LYS cc_start: 0.6756 (tmtt) cc_final: 0.6338 (mttm) outliers start: 19 outliers final: 8 residues processed: 153 average time/residue: 0.2031 time to fit residues: 42.7425 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 : 0.877 ------------------------------------------------------------------------------- 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 31 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 31 ASN L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109405 restraints weight = 11415.803| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.22 r_work: 0.3220 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8455 Z= 0.258 Angle : 0.653 7.626 11486 Z= 0.329 Chirality : 0.046 0.178 1292 Planarity : 0.004 0.048 1485 Dihedral : 10.058 106.399 1353 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.00 % Favored : 90.90 % Rotamer: Outliers : 2.02 % Allowed : 13.93 % Favored : 84.04 % 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: -3.57 (0.24), residues: 1044 helix: -3.11 (0.40), residues: 93 sheet: -2.81 (0.24), residues: 363 loop : -1.89 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.002 PHE B 308 TYR 0.025 0.002 TYR A 288 ARG 0.005 0.000 ARG A 41 *********************** 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 153 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8566 (tm-30) REVERT: H 10 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8070 (mm-30) REVERT: H 23 LYS cc_start: 0.8411 (tppt) cc_final: 0.7837 (tptp) REVERT: L 61 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7866 (mtm-85) REVERT: A 208 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.8005 (mmt-90) REVERT: A 285 MET cc_start: 0.8881 (mtp) cc_final: 0.8646 (mtm) REVERT: B 390 LYS cc_start: 0.6613 (tmtt) cc_final: 0.6135 (mttm) outliers start: 18 outliers final: 13 residues processed: 143 average time/residue: 0.2414 time to fit residues: 46.8977 Evaluate side-chains 137 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 L residue 6 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 172 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 31 ASN 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 = 0.3641 r_free = 0.3641 target = 0.134842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107864 restraints weight = 11428.503| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.22 r_work: 0.3197 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8455 Z= 0.318 Angle : 0.682 9.473 11486 Z= 0.340 Chirality : 0.049 0.439 1292 Planarity : 0.004 0.048 1485 Dihedral : 9.805 104.725 1351 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.92 % Allowed : 15.39 % Favored : 81.69 % 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: -3.49 (0.24), residues: 1044 helix: -3.03 (0.40), residues: 93 sheet: -2.77 (0.25), residues: 363 loop : -1.83 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 107 HIS 0.008 0.001 HIS A 338 PHE 0.015 0.002 PHE B 100 TYR 0.025 0.002 TYR A 288 ARG 0.005 0.000 ARG A 41 *********************** 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 154 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8607 (tm-30) REVERT: H 23 LYS cc_start: 0.8413 (tppt) cc_final: 0.7846 (tptp) REVERT: L 61 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: A 208 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.8010 (mmt-90) REVERT: B 390 LYS cc_start: 0.6601 (tmtt) cc_final: 0.6117 (mttm) REVERT: B 400 GLU cc_start: 0.7883 (tt0) cc_final: 0.7550 (mm-30) outliers start: 26 outliers final: 17 residues processed: 139 average time/residue: 0.2327 time to fit residues: 43.7027 Evaluate side-chains 138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL 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 Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** L 27 GLN L 31 ASN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109986 restraints weight = 11163.688| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.20 r_work: 0.3226 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8455 Z= 0.239 Angle : 0.634 8.093 11486 Z= 0.317 Chirality : 0.046 0.188 1292 Planarity : 0.004 0.047 1485 Dihedral : 11.205 118.346 1351 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.81 % Allowed : 16.40 % Favored : 80.79 % 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: -3.32 (0.25), residues: 1044 helix: -2.83 (0.42), residues: 91 sheet: -2.64 (0.25), residues: 366 loop : -1.73 (0.25), residues: 587 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 0.001 PHE B 100 TYR 0.020 0.002 TYR A 288 ARG 0.007 0.000 ARG A 41 *********************** 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 162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8565 (tm-30) REVERT: H 10 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8130 (mm-30) REVERT: H 23 LYS cc_start: 0.8384 (tppt) cc_final: 0.7829 (tptp) REVERT: H 69 THR cc_start: 0.8244 (m) cc_final: 0.8036 (p) REVERT: L 61 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: A 208 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.8012 (mmt-90) REVERT: A 285 MET cc_start: 0.8923 (mtm) cc_final: 0.8675 (mtm) REVERT: B 124 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7917 (mmt) REVERT: B 390 LYS cc_start: 0.6613 (tmtt) cc_final: 0.6101 (mttm) REVERT: B 400 GLU cc_start: 0.7828 (tt0) cc_final: 0.7502 (mm-30) outliers start: 25 outliers final: 18 residues processed: 146 average time/residue: 0.2191 time to fit residues: 43.4551 Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 31 ASN 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 42 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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** L 38 GLN 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 = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109482 restraints weight = 11323.646| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.23 r_work: 0.3220 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8455 Z= 0.257 Angle : 0.644 8.885 11486 Z= 0.318 Chirality : 0.046 0.270 1292 Planarity : 0.004 0.046 1485 Dihedral : 10.353 102.657 1351 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.03 % Allowed : 16.74 % Favored : 80.22 % 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: -3.28 (0.25), residues: 1044 helix: -2.74 (0.42), residues: 91 sheet: -2.59 (0.25), residues: 370 loop : -1.72 (0.26), residues: 583 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 0.015 0.001 PHE B 100 TYR 0.019 0.002 TYR A 288 ARG 0.007 0.000 ARG A 41 *********************** 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 164 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8600 (tt0) REVERT: H 47 TRP cc_start: 0.8016 (OUTLIER) cc_final: 0.7630 (t60) REVERT: L 61 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7713 (mtm-85) REVERT: A 208 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.7988 (mmt-90) REVERT: A 285 MET cc_start: 0.8954 (mtm) cc_final: 0.8751 (mtm) REVERT: B 124 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7923 (mmt) REVERT: B 390 LYS cc_start: 0.6618 (tmtt) cc_final: 0.6105 (mttm) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.2117 time to fit residues: 43.8034 Evaluate side-chains 150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 42 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** L 27 GLN L 31 ASN L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111052 restraints weight = 11344.320| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.32 r_work: 0.3227 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8455 Z= 0.223 Angle : 0.637 8.304 11486 Z= 0.316 Chirality : 0.045 0.183 1292 Planarity : 0.004 0.046 1485 Dihedral : 10.869 119.365 1351 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.48 % Allowed : 17.87 % Favored : 78.65 % 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: -3.18 (0.25), residues: 1044 helix: -2.62 (0.42), residues: 91 sheet: -2.50 (0.25), residues: 366 loop : -1.69 (0.26), residues: 587 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 0.012 0.001 PHE B 100 TYR 0.018 0.001 TYR A 288 ARG 0.007 0.000 ARG H 84 *********************** 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 169 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8581 (tpp) cc_final: 0.8301 (mmm) REVERT: H 47 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.7627 (t60) REVERT: L 61 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7712 (mtm-85) REVERT: A 208 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.8009 (mmt-90) REVERT: A 259 THR cc_start: 0.9115 (m) cc_final: 0.8645 (p) REVERT: B 124 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7915 (mmt) REVERT: B 253 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8414 (mtmm) REVERT: B 390 LYS cc_start: 0.6666 (tmtt) cc_final: 0.6169 (mttm) REVERT: B 400 GLU cc_start: 0.7873 (tt0) cc_final: 0.7467 (mm-30) outliers start: 31 outliers final: 22 residues processed: 152 average time/residue: 0.2071 time to fit residues: 43.2156 Evaluate side-chains 147 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 58 VAL 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 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 253 LYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108215 restraints weight = 11571.060| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.27 r_work: 0.3191 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8455 Z= 0.333 Angle : 0.677 8.732 11486 Z= 0.334 Chirality : 0.048 0.378 1292 Planarity : 0.004 0.042 1485 Dihedral : 9.169 101.155 1351 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.48 % Allowed : 19.66 % Favored : 76.85 % 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: -3.13 (0.25), residues: 1044 helix: -2.61 (0.41), residues: 91 sheet: -2.44 (0.25), residues: 367 loop : -1.68 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.008 0.001 HIS A 338 PHE 0.015 0.002 PHE B 308 TYR 0.025 0.002 TYR A 288 ARG 0.005 0.000 ARG A 41 *********************** 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 162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8617 (tpp) cc_final: 0.8344 (mmm) REVERT: H 47 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.7658 (t60) REVERT: L 61 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7745 (mtm-85) REVERT: A 208 ARG cc_start: 0.8426 (mmt-90) cc_final: 0.8084 (mmt-90) REVERT: A 285 MET cc_start: 0.9023 (mtm) cc_final: 0.8784 (ttm) REVERT: B 124 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7861 (mmt) REVERT: B 149 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8216 (pt) REVERT: B 253 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8364 (mtmm) REVERT: B 390 LYS cc_start: 0.6552 (tmtt) cc_final: 0.6082 (mttm) outliers start: 31 outliers final: 22 residues processed: 148 average time/residue: 0.1986 time to fit residues: 40.5969 Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 58 VAL 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 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 406 VAL 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 253 LYS Chi-restraints excluded: chain B residue 311 THR 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: 1.9990 chunk 73 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** L 27 GLN L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110672 restraints weight = 11490.528| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.11 r_work: 0.3241 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8455 Z= 0.235 Angle : 0.653 8.993 11486 Z= 0.324 Chirality : 0.046 0.216 1292 Planarity : 0.004 0.043 1485 Dihedral : 10.331 114.104 1351 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.26 % Allowed : 19.89 % Favored : 76.85 % 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: -3.04 (0.25), residues: 1044 helix: -2.47 (0.43), residues: 91 sheet: -2.34 (0.26), residues: 360 loop : -1.68 (0.26), residues: 593 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 0.011 0.001 PHE A 171 TYR 0.019 0.001 TYR A 288 ARG 0.005 0.000 ARG A 41 *********************** 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 161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7636 (t60) REVERT: L 61 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7736 (mtm-85) REVERT: A 208 ARG cc_start: 0.8427 (mmt-90) cc_final: 0.8095 (mmt-90) REVERT: A 285 MET cc_start: 0.9009 (mtm) cc_final: 0.8771 (ttm) REVERT: B 124 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: B 149 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8225 (pt) REVERT: B 253 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: B 390 LYS cc_start: 0.6648 (tmtt) cc_final: 0.6160 (mttm) REVERT: B 400 GLU cc_start: 0.7837 (tt0) cc_final: 0.7431 (mm-30) outliers start: 29 outliers final: 22 residues processed: 145 average time/residue: 0.2487 time to fit residues: 49.3159 Evaluate side-chains 153 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 42 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 293 VAL 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 253 LYS Chi-restraints excluded: chain B residue 311 THR 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: 3.9990 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109436 restraints weight = 11404.553| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.24 r_work: 0.3218 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8455 Z= 0.275 Angle : 0.658 8.586 11486 Z= 0.325 Chirality : 0.047 0.337 1292 Planarity : 0.004 0.044 1485 Dihedral : 8.482 100.151 1351 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 3.37 % Allowed : 19.78 % Favored : 76.85 % 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: -3.01 (0.25), residues: 1044 helix: -2.43 (0.43), residues: 91 sheet: -2.34 (0.26), residues: 344 loop : -1.69 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.002 PHE B 100 TYR 0.021 0.002 TYR A 288 ARG 0.005 0.000 ARG A 41 ********************** 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 157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: H 10 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8053 (mm-30) REVERT: H 47 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.7601 (t60) REVERT: H 60 TYR cc_start: 0.8157 (m-80) cc_final: 0.7946 (m-80) REVERT: A 208 ARG cc_start: 0.8436 (mmt-90) cc_final: 0.8098 (mmt-90) REVERT: A 259 THR cc_start: 0.9139 (m) cc_final: 0.8666 (p) REVERT: B 124 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7832 (mmt) REVERT: B 149 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8210 (pt) REVERT: B 253 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: B 390 LYS cc_start: 0.6685 (tmtt) cc_final: 0.6197 (mttm) outliers start: 30 outliers final: 22 residues processed: 141 average time/residue: 0.2032 time to fit residues: 39.5683 Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 42 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 293 VAL 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 253 LYS Chi-restraints excluded: chain B residue 311 THR 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: 0.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 39 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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** L 38 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.138129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111318 restraints weight = 11477.074| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.26 r_work: 0.3234 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8455 Z= 0.208 Angle : 0.644 9.007 11486 Z= 0.318 Chirality : 0.045 0.202 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.886 115.861 1351 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.92 % Allowed : 19.89 % Favored : 77.19 % 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: -2.90 (0.25), residues: 1044 helix: -2.17 (0.45), residues: 88 sheet: -2.27 (0.27), residues: 343 loop : -1.64 (0.25), residues: 613 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 0.010 0.001 PHE A 171 TYR 0.017 0.001 TYR A 288 ARG 0.007 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4845.51 seconds wall clock time: 84 minutes 28.45 seconds (5068.45 seconds total)