Starting phenix.real_space_refine on Tue Sep 24 16:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/09_2024/7la4_23245.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/09_2024/7la4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/09_2024/7la4_23245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/09_2024/7la4_23245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/09_2024/7la4_23245.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/09_2024/7la4_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.85, per 1000 atoms: 0.71 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: 2.32 Conformation dependent library (CDL) restraints added in 940.3 milliseconds 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: 1.02 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: 2.29 Time building geometry restraints manager: 2.67 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: 2.710 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: 0.070 Set scattering table: 0.090 Process input model: 22.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.112 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: 0.2304 time to fit residues: 49.4391 Evaluate side-chains 121 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7981 (mtm-85) REVERT: A 285 MET cc_start: 0.8522 (mtp) cc_final: 0.8165 (mtm) REVERT: B 390 LYS cc_start: 0.6510 (tmtt) cc_final: 0.6216 (mttm) outliers start: 19 outliers final: 8 residues processed: 153 average time/residue: 0.2081 time to fit residues: 43.7360 Evaluate side-chains 136 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8455 Z= 0.273 Angle : 0.656 7.525 11486 Z= 0.330 Chirality : 0.046 0.176 1292 Planarity : 0.004 0.048 1485 Dihedral : 10.068 106.349 1353 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.29 % Favored : 90.61 % Rotamer: Outliers : 2.02 % Allowed : 14.16 % Favored : 83.82 % 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: -3.59 (0.24), residues: 1044 helix: -3.13 (0.40), residues: 93 sheet: -2.82 (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 0.014 0.002 PHE B 308 TYR 0.027 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 fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8384 (tm-30) REVERT: H 23 LYS cc_start: 0.8346 (tppt) cc_final: 0.8125 (tptp) REVERT: L 61 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: L 106 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7903 (pp) REVERT: A 208 ARG cc_start: 0.8064 (mmt-90) cc_final: 0.7827 (mmt-90) REVERT: A 285 MET cc_start: 0.8571 (mtp) cc_final: 0.8312 (mtm) REVERT: B 390 LYS cc_start: 0.6510 (tmtt) cc_final: 0.6207 (mttm) outliers start: 18 outliers final: 13 residues processed: 143 average time/residue: 0.2310 time to fit residues: 45.0295 Evaluate side-chains 137 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 L residue 106 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 92 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8455 Z= 0.249 Angle : 0.660 9.485 11486 Z= 0.329 Chirality : 0.048 0.394 1292 Planarity : 0.004 0.048 1485 Dihedral : 9.851 104.836 1353 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.70 % Allowed : 15.73 % Favored : 81.57 % 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: -3.46 (0.24), residues: 1044 helix: -3.01 (0.40), residues: 93 sheet: -2.73 (0.25), residues: 363 loop : -1.81 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 107 HIS 0.007 0.001 HIS A 338 PHE 0.012 0.002 PHE B 308 TYR 0.021 0.002 TYR A 288 ARG 0.006 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 153 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8354 (tm-30) REVERT: H 23 LYS cc_start: 0.8319 (tppt) cc_final: 0.8107 (tptp) REVERT: L 61 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: L 106 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7924 (pp) REVERT: A 208 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7823 (mmt-90) REVERT: B 390 LYS cc_start: 0.6485 (tmtt) cc_final: 0.6183 (mttm) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 0.2199 time to fit residues: 41.4403 Evaluate side-chains 137 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 L residue 106 ILE 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 82 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 0 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8455 Z= 0.264 Angle : 0.638 8.316 11486 Z= 0.318 Chirality : 0.045 0.181 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.469 103.168 1353 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.92 % Allowed : 16.29 % Favored : 80.79 % 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: -3.32 (0.25), residues: 1044 helix: -2.84 (0.41), residues: 91 sheet: -2.63 (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 0.012 0.002 PHE B 308 TYR 0.023 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 167 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8331 (tm-30) REVERT: H 23 LYS cc_start: 0.8308 (tppt) cc_final: 0.8096 (tptp) REVERT: L 106 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 208 ARG cc_start: 0.8061 (mmt-90) cc_final: 0.7830 (mmt-90) REVERT: A 285 MET cc_start: 0.8707 (mtm) cc_final: 0.8493 (mtm) REVERT: B 124 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8061 (mmt) REVERT: B 390 LYS cc_start: 0.6545 (tmtt) cc_final: 0.6211 (mttm) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 0.2157 time to fit residues: 43.5691 Evaluate side-chains 142 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 H residue 97 THR 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 L residue 106 ILE Chi-restraints excluded: chain A residue 37 VAL 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 33 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 38 GLN B 280 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8455 Z= 0.323 Angle : 0.666 8.417 11486 Z= 0.331 Chirality : 0.046 0.180 1292 Planarity : 0.004 0.045 1485 Dihedral : 9.314 102.047 1353 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.60 % Allowed : 16.97 % Favored : 79.44 % 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: -3.29 (0.25), residues: 1044 helix: -2.76 (0.42), residues: 91 sheet: -2.60 (0.25), residues: 370 loop : -1.72 (0.26), residues: 583 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 0.014 0.002 PHE A 171 TYR 0.027 0.002 TYR A 288 ARG 0.007 0.000 ARG H 84 *********************** 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 162 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 0.982 Fit side-chains REVERT: H 5 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8283 (tt0) REVERT: H 34 MET cc_start: 0.7585 (tpp) cc_final: 0.7363 (mmm) REVERT: B 124 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8109 (mmt) REVERT: B 390 LYS cc_start: 0.6435 (tmtt) cc_final: 0.6154 (mttm) outliers start: 32 outliers final: 23 residues processed: 144 average time/residue: 0.2119 time to fit residues: 42.2303 Evaluate side-chains 142 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 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 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 27 GLN 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 37 VAL 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 404 SER 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 387 MET 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 96 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8455 Z= 0.326 Angle : 0.676 8.348 11486 Z= 0.336 Chirality : 0.047 0.318 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.346 101.830 1351 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.82 % Allowed : 17.75 % Favored : 78.43 % 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: -3.25 (0.25), residues: 1044 helix: -2.70 (0.42), residues: 91 sheet: -2.53 (0.25), residues: 364 loop : -1.74 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.008 0.001 HIS A 338 PHE 0.014 0.002 PHE A 171 TYR 0.024 0.002 TYR A 288 ARG 0.006 0.000 ARG A 41 *********************** 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 161 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.029 Fit side-chains REVERT: H 5 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8268 (tt0) REVERT: H 34 MET cc_start: 0.7580 (tpp) cc_final: 0.7339 (mmm) REVERT: B 124 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7968 (mmt) REVERT: B 127 ASP cc_start: 0.6651 (m-30) cc_final: 0.5954 (m-30) REVERT: B 149 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8257 (pt) REVERT: B 390 LYS cc_start: 0.6442 (tmtt) cc_final: 0.6172 (mttm) outliers start: 34 outliers final: 27 residues processed: 144 average time/residue: 0.2110 time to fit residues: 41.8892 Evaluate side-chains 146 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 27 GLN 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 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 404 SER 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 423 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2349 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= 0.259 Angle : 0.667 10.771 11486 Z= 0.330 Chirality : 0.046 0.217 1292 Planarity : 0.004 0.046 1485 Dihedral : 10.166 101.488 1351 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 3.26 % Allowed : 19.33 % Favored : 77.42 % 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: -2.65 (0.42), residues: 91 sheet: -2.46 (0.26), residues: 358 loop : -1.74 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.006 0.001 HIS A 338 PHE 0.012 0.002 PHE B 308 TYR 0.019 0.002 TYR A 288 ARG 0.008 0.000 ARG A 208 *********************** 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 158 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8259 (tt0) REVERT: B 124 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8032 (mmt) REVERT: B 149 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8211 (pt) REVERT: B 187 MET cc_start: 0.7284 (ttm) cc_final: 0.7054 (ttt) REVERT: B 390 LYS cc_start: 0.6424 (tmtt) cc_final: 0.6160 (mttm) outliers start: 29 outliers final: 23 residues processed: 144 average time/residue: 0.1997 time to fit residues: 40.3802 Evaluate side-chains 145 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0870 chunk 92 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2504 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= 0.210 Angle : 0.648 9.152 11486 Z= 0.320 Chirality : 0.046 0.302 1292 Planarity : 0.004 0.044 1485 Dihedral : 8.682 100.641 1351 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.92 % Allowed : 19.66 % Favored : 77.42 % 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: -3.03 (0.25), residues: 1044 helix: -2.41 (0.44), residues: 88 sheet: -2.36 (0.26), residues: 340 loop : -1.72 (0.25), residues: 616 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 0.012 0.001 PHE B 100 TYR 0.016 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 158 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8241 (tt0) REVERT: L 61 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7852 (mtm-85) REVERT: A 259 THR cc_start: 0.8612 (m) cc_final: 0.8232 (p) REVERT: B 390 LYS cc_start: 0.6558 (tmtt) cc_final: 0.6272 (mttm) outliers start: 26 outliers final: 20 residues processed: 144 average time/residue: 0.2168 time to fit residues: 43.4229 Evaluate side-chains 143 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 6 GLN 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 430 ASN Chi-restraints excluded: chain B residue 118 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.0870 chunk 94 optimal weight: 0.0970 chunk 81 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8455 Z= 0.206 Angle : 0.654 9.533 11486 Z= 0.324 Chirality : 0.046 0.286 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.966 111.142 1351 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.36 % Allowed : 20.34 % Favored : 77.30 % 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: -3.01 (0.25), residues: 1044 helix: -2.37 (0.43), residues: 91 sheet: -2.31 (0.27), residues: 340 loop : -1.71 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.005 0.001 HIS A 338 PHE 0.010 0.001 PHE B 308 TYR 0.015 0.001 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 143 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: L 61 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7833 (mtm-85) REVERT: A 259 THR cc_start: 0.8627 (m) cc_final: 0.8274 (p) REVERT: B 149 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8226 (pt) REVERT: B 187 MET cc_start: 0.7017 (tpp) cc_final: 0.6683 (ttt) REVERT: B 390 LYS cc_start: 0.6491 (tmtt) cc_final: 0.6256 (mttm) outliers start: 21 outliers final: 19 residues processed: 133 average time/residue: 0.1933 time to fit residues: 36.3112 Evaluate side-chains 140 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 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 149 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3637 r_free = 0.3637 target = 0.134748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108473 restraints weight = 11314.514| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.09 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8455 Z= 0.340 Angle : 0.680 8.390 11486 Z= 0.337 Chirality : 0.047 0.311 1292 Planarity : 0.004 0.043 1485 Dihedral : 8.297 99.209 1351 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 2.81 % Allowed : 20.00 % Favored : 77.19 % 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: -3.07 (0.25), residues: 1044 helix: -2.39 (0.42), residues: 91 sheet: -2.33 (0.26), residues: 358 loop : -1.73 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 100 HIS 0.008 0.001 HIS A 338 PHE 0.016 0.002 PHE B 100 TYR 0.024 0.002 TYR A 288 ARG 0.005 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.29 seconds wall clock time: 39 minutes 30.80 seconds (2370.80 seconds total)