Starting phenix.real_space_refine on Mon Mar 11 12:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/03_2024/7la4_23245.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/03_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_23245/03_2024/7la4_23245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/03_2024/7la4_23245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/03_2024/7la4_23245.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7la4_23245/03_2024/7la4_23245.pdb" } 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 Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.36, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 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: 0.86 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: 2.24 Time building geometry restraints manager: 3.47 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: 98.48 - 105.59: 194 105.59 - 112.70: 4422 112.70 - 119.81: 2746 119.81 - 126.92: 4019 126.92 - 134.04: 105 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 2.440 nonbonded pdb=" OH TYR A 353 " pdb=" OE1 GLU B 297 " model vdw 2.138 2.440 nonbonded pdb=" OG SER A 22 " pdb=" O GLY A 94 " model vdw 2.156 2.440 nonbonded pdb=" OE1 GLN A 197 " pdb=" OG SER A 220 " model vdw 2.159 2.440 ... (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 ========== 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: 4.240 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: 7.680 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.690 Find NCS groups from input model: 0.240 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 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 : 0.978 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: 0.2192 time to fit residues: 46.8400 Evaluate side-chains 121 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8455 Z= 0.258 Angle : 0.662 7.446 11486 Z= 0.336 Chirality : 0.048 0.366 1292 Planarity : 0.004 0.045 1485 Dihedral : 10.938 105.865 1355 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.29 % Favored : 90.52 % Rotamer: Outliers : 2.25 % Allowed : 10.22 % Favored : 87.53 % 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: -3.79 (0.24), residues: 1044 helix: -3.53 (0.36), residues: 98 sheet: -2.85 (0.25), residues: 365 loop : -2.04 (0.25), residues: 581 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 0.002 PHE A 87 TYR 0.030 0.002 TYR A 288 ARG 0.005 0.000 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 156 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7795 (pp) REVERT: A 285 MET cc_start: 0.8581 (mtp) cc_final: 0.8192 (mtm) outliers start: 20 outliers final: 9 residues processed: 144 average time/residue: 0.1989 time to fit residues: 39.5573 Evaluate side-chains 130 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 31 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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: 0.8016 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8455 Z= 0.301 Angle : 0.647 7.566 11486 Z= 0.327 Chirality : 0.047 0.371 1292 Planarity : 0.004 0.045 1485 Dihedral : 10.499 103.780 1353 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.39 % Favored : 90.42 % Rotamer: Outliers : 2.25 % Allowed : 13.93 % 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: -3.65 (0.24), residues: 1044 helix: -3.28 (0.38), residues: 98 sheet: -2.83 (0.25), residues: 365 loop : -1.91 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.013 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 151 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8329 (tm-30) REVERT: L 106 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 270 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7827 (pp) REVERT: A 285 MET cc_start: 0.8591 (mtp) cc_final: 0.8305 (mtm) REVERT: B 124 MET cc_start: 0.8385 (tpt) cc_final: 0.8126 (mmt) REVERT: B 390 LYS cc_start: 0.6528 (tmtt) cc_final: 0.6172 (mttp) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.2058 time to fit residues: 40.3829 Evaluate side-chains 142 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain H residue 71 THR 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 70 ASP Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 270 LEU 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: 1.9990 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN L 37 GLN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8455 Z= 0.294 Angle : 0.637 7.870 11486 Z= 0.321 Chirality : 0.047 0.312 1292 Planarity : 0.004 0.046 1485 Dihedral : 10.198 101.932 1353 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.26 % Allowed : 15.28 % Favored : 81.46 % 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: -3.60 (0.24), residues: 1044 helix: -3.18 (0.39), residues: 99 sheet: -2.77 (0.25), residues: 355 loop : -1.94 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.007 0.001 HIS A 338 PHE 0.013 0.002 PHE B 308 TYR 0.024 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 162 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8335 (tm-30) REVERT: L 106 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (pp) REVERT: A 270 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7788 (pp) REVERT: B 390 LYS cc_start: 0.6516 (tmtt) cc_final: 0.6166 (mttm) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2085 time to fit residues: 41.7259 Evaluate side-chains 149 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 69 THR 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 31 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 70 ASP 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 270 LEU 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 387 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: 0.0470 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 89 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8455 Z= 0.184 Angle : 0.597 8.231 11486 Z= 0.300 Chirality : 0.045 0.368 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.834 100.507 1353 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.58 % Allowed : 16.40 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.25), residues: 1044 helix: -2.72 (0.43), residues: 91 sheet: -2.63 (0.25), residues: 365 loop : -1.77 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 235 HIS 0.006 0.001 HIS A 338 PHE 0.010 0.001 PHE B 308 TYR 0.016 0.001 TYR A 288 ARG 0.006 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 168 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8320 (tt0) REVERT: L 90 GLN cc_start: 0.8065 (pp30) cc_final: 0.7478 (pt0) REVERT: L 106 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8089 (pp) REVERT: A 259 THR cc_start: 0.8726 (m) cc_final: 0.8292 (p) REVERT: A 285 MET cc_start: 0.8604 (mtm) cc_final: 0.8331 (mtm) REVERT: B 390 LYS cc_start: 0.6562 (tmtt) cc_final: 0.6182 (mttm) outliers start: 23 outliers final: 15 residues processed: 153 average time/residue: 0.2033 time to fit residues: 43.1152 Evaluate side-chains 145 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 70 ASP 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 166 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8455 Z= 0.240 Angle : 0.603 8.444 11486 Z= 0.301 Chirality : 0.045 0.327 1292 Planarity : 0.004 0.046 1485 Dihedral : 9.603 99.642 1353 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.70 % Allowed : 18.20 % Favored : 79.10 % 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: -3.26 (0.25), residues: 1044 helix: -2.62 (0.43), residues: 91 sheet: -2.54 (0.25), residues: 367 loop : -1.76 (0.25), residues: 586 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 308 TYR 0.020 0.001 TYR A 288 ARG 0.006 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 160 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8315 (tt0) REVERT: L 106 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8286 (pp) REVERT: A 270 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7706 (pp) REVERT: A 285 MET cc_start: 0.8698 (mtm) cc_final: 0.8452 (mtm) REVERT: B 124 MET cc_start: 0.8720 (mmt) cc_final: 0.8348 (mmt) REVERT: B 390 LYS cc_start: 0.6551 (tmtt) cc_final: 0.6183 (mttm) outliers start: 24 outliers final: 17 residues processed: 145 average time/residue: 0.1960 time to fit residues: 40.3827 Evaluate side-chains 146 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 69 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 39 LYS 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 42 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 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 96 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8455 Z= 0.235 Angle : 0.608 8.484 11486 Z= 0.305 Chirality : 0.046 0.371 1292 Planarity : 0.004 0.043 1485 Dihedral : 9.427 98.648 1353 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.92 % Allowed : 18.99 % Favored : 78.09 % 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: -3.20 (0.25), residues: 1044 helix: -2.45 (0.43), residues: 92 sheet: -2.48 (0.25), residues: 367 loop : -1.76 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 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 163 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8298 (tt0) REVERT: L 106 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8356 (pp) REVERT: A 270 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7705 (pp) REVERT: A 285 MET cc_start: 0.8727 (mtm) cc_final: 0.8501 (mtm) REVERT: B 141 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: B 390 LYS cc_start: 0.6625 (tmtt) cc_final: 0.6220 (mttp) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.2160 time to fit residues: 44.4757 Evaluate side-chains 150 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 39 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 70 ASP 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 42 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 141 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8455 Z= 0.232 Angle : 0.607 8.482 11486 Z= 0.304 Chirality : 0.046 0.368 1292 Planarity : 0.004 0.044 1485 Dihedral : 9.223 97.836 1353 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.37 % Allowed : 18.54 % Favored : 78.09 % 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: -2.28 (0.44), residues: 92 sheet: -2.46 (0.25), residues: 359 loop : -1.73 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 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 0.009 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 160 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8257 (tt0) REVERT: H 34 MET cc_start: 0.7517 (tpp) cc_final: 0.7290 (mmm) REVERT: L 90 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: A 270 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7692 (pp) REVERT: B 124 MET cc_start: 0.8827 (mmt) cc_final: 0.8204 (mmt) REVERT: B 141 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: B 149 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8277 (pt) REVERT: B 390 LYS cc_start: 0.6661 (tmtt) cc_final: 0.6269 (mttp) outliers start: 30 outliers final: 19 residues processed: 146 average time/residue: 0.2004 time to fit residues: 40.6546 Evaluate side-chains 151 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS 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 90 GLN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 125 THR 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 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 141 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8455 Z= 0.262 Angle : 0.617 8.569 11486 Z= 0.309 Chirality : 0.046 0.354 1292 Planarity : 0.004 0.044 1485 Dihedral : 8.985 97.050 1351 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.26 % Allowed : 18.65 % Favored : 78.09 % 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: -3.10 (0.25), residues: 1044 helix: -2.19 (0.45), residues: 92 sheet: -2.44 (0.25), residues: 359 loop : -1.72 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 113 HIS 0.007 0.001 HIS A 338 PHE 0.012 0.002 PHE A 171 TYR 0.021 0.002 TYR A 288 ARG 0.007 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 fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7553 (tpp) cc_final: 0.7305 (mmm) REVERT: L 90 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7126 (pt0) REVERT: A 270 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7697 (pp) REVERT: B 124 MET cc_start: 0.8826 (mmt) cc_final: 0.8172 (mmt) REVERT: B 141 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: B 149 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8255 (pt) REVERT: B 390 LYS cc_start: 0.6614 (tmtt) cc_final: 0.6263 (mttp) outliers start: 29 outliers final: 22 residues processed: 149 average time/residue: 0.1948 time to fit residues: 40.9681 Evaluate side-chains 151 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 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 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 125 THR 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 270 LEU 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 141 GLN 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 Chi-restraints excluded: chain B residue 425 LEU 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: 1.9990 chunk 68 optimal weight: 0.0060 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8455 Z= 0.212 Angle : 0.599 8.742 11486 Z= 0.300 Chirality : 0.045 0.347 1292 Planarity : 0.004 0.045 1485 Dihedral : 8.659 96.485 1351 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.58 % Allowed : 19.33 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.25), residues: 1044 helix: -2.01 (0.47), residues: 92 sheet: -2.36 (0.26), residues: 357 loop : -1.65 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.006 0.001 HIS A 338 PHE 0.010 0.001 PHE A 171 TYR 0.014 0.001 TYR A 288 ARG 0.008 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 153 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7507 (tpp) cc_final: 0.7260 (mmm) REVERT: L 90 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6784 (pt0) REVERT: A 270 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7673 (pp) REVERT: B 124 MET cc_start: 0.8827 (mmt) cc_final: 0.8193 (mmt) REVERT: B 141 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: B 390 LYS cc_start: 0.6592 (tmtt) cc_final: 0.6255 (mttp) outliers start: 23 outliers final: 18 residues processed: 142 average time/residue: 0.2025 time to fit residues: 39.9159 Evaluate side-chains 144 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS 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 90 GLN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 141 GLN 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: 0.9980 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 4 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109601 restraints weight = 11281.909| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.25 r_work: 0.3230 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8455 Z= 0.244 Angle : 0.611 8.835 11486 Z= 0.306 Chirality : 0.046 0.338 1292 Planarity : 0.004 0.046 1485 Dihedral : 8.284 95.637 1351 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.70 % Allowed : 19.33 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.25), residues: 1044 helix: -1.91 (0.47), residues: 92 sheet: -2.36 (0.26), residues: 358 loop : -1.62 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 113 HIS 0.006 0.001 HIS A 338 PHE 0.011 0.001 PHE A 171 TYR 0.013 0.002 TYR A 288 ARG 0.007 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.10 seconds wall clock time: 39 minutes 58.26 seconds (2398.26 seconds total)