Starting phenix.real_space_refine on Fri Jul 19 17:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4i_15849/07_2024/8b4i_15849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4i_15849/07_2024/8b4i_15849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4i_15849/07_2024/8b4i_15849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4i_15849/07_2024/8b4i_15849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4i_15849/07_2024/8b4i_15849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b4i_15849/07_2024/8b4i_15849.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 C 5322 2.51 5 N 1347 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8242 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} Conformer: "B" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} bond proxies already assigned to first conformer: 2547 Chain: "B" Number of atoms: 2515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} Conformer: "B" Number of residues, atoms: 325, 2507 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 315} bond proxies already assigned to first conformer: 2547 Chain: "C" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 450 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 450 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 290 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "F" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 290 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 289 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "H" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 289 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "J" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'DU0': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'DU0': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {'DU0': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.97, per 1000 atoms: 0.97 Number of scatterers: 8242 At special positions: 0 Unit cell: (123.876, 106.299, 99.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 1 15.00 O 1548 8.00 N 1347 7.00 C 5322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 2.1 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 38.9% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.832A pdb=" N PHE A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 334 through 343 removed outlier: 4.345A pdb=" N GLU A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 334 through 343 removed outlier: 4.344A pdb=" N GLU B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLY B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 122 Proline residue: C 99 - end of helix Processing helix chain 'D' and resid 64 through 122 Proline residue: D 99 - end of helix Processing helix chain 'E' and resid 11 through 46 Proline residue: E 40 - end of helix Processing helix chain 'F' and resid 11 through 46 Proline residue: F 40 - end of helix Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.978A pdb=" N THR G 28 " --> pdb=" O TYR G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 Processing helix chain 'G' and resid 52 through 58 Processing helix chain 'H' and resid 23 through 28 removed outlier: 4.072A pdb=" N THR H 28 " --> pdb=" O TYR H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 50 removed outlier: 4.727A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 58 Processing helix chain 'I' and resid 5 through 39 removed outlier: 3.655A pdb=" N ARG I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU I 28 " --> pdb=" O HIS I 24 " (cutoff:3.500A) Proline residue: I 29 - end of helix Processing helix chain 'I' and resid 44 through 49 removed outlier: 3.775A pdb=" N LEU I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU I 49 " --> pdb=" O ILE I 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 44 through 49' Processing helix chain 'J' and resid 5 through 39 removed outlier: 3.552A pdb=" N ARG J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU J 28 " --> pdb=" O HIS J 24 " (cutoff:3.500A) Proline residue: J 29 - end of helix Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.922A pdb=" N LEU J 49 " --> pdb=" O ILE J 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 74 removed outlier: 6.345A pdb=" N PHE A 79 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 135 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 147 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA A 144 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 159 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR A 172 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 207 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 319 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY A 64 " --> pdb=" O MET A 324 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 326 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 66 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 328 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP A 68 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA A 330 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 70 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 74 removed outlier: 6.295A pdb=" N PHE B 79 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE B 135 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA B 144 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 172 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 207 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 319 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY B 64 " --> pdb=" O MET B 324 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL B 326 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B 66 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 328 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 68 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA B 330 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 70 " --> pdb=" O ALA B 330 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1600 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: 2.32 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1384 1.32 - 1.44: 2230 1.44 - 1.56: 4773 1.56 - 1.68: 2 1.68 - 1.80: 46 Bond restraints: 8435 Sorted by residual: bond pdb=" C22 DU0 B 402 " pdb=" O23 DU0 B 402 " ideal model delta sigma weight residual 1.412 1.439 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C22 DU0 A 401 " pdb=" O23 DU0 A 401 " ideal model delta sigma weight residual 1.412 1.437 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C09 DU0 C 201 " pdb=" O16 DU0 C 201 " ideal model delta sigma weight residual 1.404 1.429 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C09 DU0 B 402 " pdb=" O16 DU0 B 402 " ideal model delta sigma weight residual 1.404 1.428 -0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" C24 DU0 C 201 " pdb=" O23 DU0 C 201 " ideal model delta sigma weight residual 1.409 1.433 -0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 8430 not shown) Histogram of bond angle deviations from ideal: 94.13 - 102.10: 40 102.10 - 110.08: 1563 110.08 - 118.05: 4934 118.05 - 126.02: 4862 126.02 - 133.99: 88 Bond angle restraints: 11487 Sorted by residual: angle pdb=" N SER A 288 " pdb=" CA SER A 288 " pdb=" C SER A 288 " ideal model delta sigma weight residual 113.28 110.33 2.95 1.22e+00 6.72e-01 5.84e+00 angle pdb=" N SER B 288 " pdb=" CA SER B 288 " pdb=" C SER B 288 " ideal model delta sigma weight residual 113.28 110.35 2.93 1.22e+00 6.72e-01 5.76e+00 angle pdb=" O10 DU0 C 201 " pdb=" C09 DU0 C 201 " pdb=" O16 DU0 C 201 " ideal model delta sigma weight residual 110.24 103.23 7.01 3.00e+00 1.11e-01 5.46e+00 angle pdb=" O10 DU0 D 201 " pdb=" C09 DU0 D 201 " pdb=" O16 DU0 D 201 " ideal model delta sigma weight residual 110.24 103.50 6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" O10 DU0 C 202 " pdb=" C09 DU0 C 202 " pdb=" O16 DU0 C 202 " ideal model delta sigma weight residual 110.24 103.85 6.39 3.00e+00 1.11e-01 4.53e+00 ... (remaining 11482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 5349 25.75 - 51.50: 108 51.50 - 77.25: 43 77.25 - 103.00: 36 103.00 - 128.74: 13 Dihedral angle restraints: 5549 sinusoidal: 2597 harmonic: 2952 Sorted by residual: dihedral pdb=" C76 DU0 D 201 " pdb=" C22 DU0 D 201 " pdb=" C75 DU0 D 201 " pdb=" O23 DU0 D 201 " ideal model delta sinusoidal sigma weight residual -179.09 -50.35 -128.74 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C76 DU0 C 201 " pdb=" C22 DU0 C 201 " pdb=" C75 DU0 C 201 " pdb=" O23 DU0 C 201 " ideal model delta sinusoidal sigma weight residual -179.09 -50.59 -128.50 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C21 DU0 D 201 " pdb=" C22 DU0 D 201 " pdb=" C75 DU0 D 201 " pdb=" C76 DU0 D 201 " ideal model delta sinusoidal sigma weight residual 56.15 -68.09 124.24 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 5546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 983 0.039 - 0.077: 256 0.077 - 0.116: 55 0.116 - 0.154: 15 0.154 - 0.193: 12 Chirality restraints: 1321 Sorted by residual: chirality pdb=" C07 DU0 C 203 " pdb=" C06 DU0 C 203 " pdb=" C08 DU0 C 203 " pdb=" C09 DU0 C 203 " both_signs ideal model delta sigma weight residual False 2.56 2.76 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" C07 DU0 D 203 " pdb=" C06 DU0 D 203 " pdb=" C08 DU0 D 203 " pdb=" C09 DU0 D 203 " both_signs ideal model delta sigma weight residual False 2.56 2.75 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" C07 DU0 A 401 " pdb=" C06 DU0 A 401 " pdb=" C08 DU0 A 401 " pdb=" C09 DU0 A 401 " both_signs ideal model delta sigma weight residual False 2.56 2.75 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1318 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 28 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO I 29 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 29 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 40 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO J 41 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 40 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 41 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.016 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1013 2.74 - 3.28: 8101 3.28 - 3.82: 12385 3.82 - 4.36: 14931 4.36 - 4.90: 27112 Nonbonded interactions: 63542 Sorted by model distance: nonbonded pdb=" O GLY I 35 " pdb=" OG SER I 39 " model vdw 2.205 2.440 nonbonded pdb=" O23 DU0 D 202 " pdb=" O52 DU0 D 202 " model vdw 2.210 2.440 nonbonded pdb=" NZ LYS A 132 " pdb=" OE1 GLU A 149 " model vdw 2.238 2.520 nonbonded pdb=" N GLN A 228 " pdb=" OE1 GLN A 228 " model vdw 2.250 2.520 nonbonded pdb=" O GLY J 35 " pdb=" OG SER J 39 " model vdw 2.271 2.440 ... (remaining 63537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 308 or resid 310 through 349)) selection = (chain 'B' and (resid 25 through 308 or resid 310 through 349)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 4.220 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.950 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.004 0.027 8435 Z= 0.289 Angle : 0.618 7.008 11487 Z= 0.310 Chirality : 0.041 0.193 1321 Planarity : 0.003 0.029 1412 Dihedral : 16.412 128.745 3649 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.24 % Allowed : 2.68 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 1008 helix: 2.10 (0.27), residues: 352 sheet: -0.41 (0.26), residues: 398 loop : -0.48 (0.46), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 236 HIS 0.002 0.001 HIS I 24 PHE 0.008 0.001 PHE A 271 TYR 0.007 0.001 TYR H 24 ARG 0.002 0.000 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 49 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8227 (ptt-90) REVERT: A 143 MET cc_start: 0.8488 (ttp) cc_final: 0.7991 (tmm) REVERT: A 215 LYS cc_start: 0.8861 (tttt) cc_final: 0.8638 (tttm) REVERT: A 321 LYS cc_start: 0.8521 (mttt) cc_final: 0.8212 (mtmt) REVERT: A 329 GLU cc_start: 0.8222 (tt0) cc_final: 0.7891 (mt-10) REVERT: B 215 LYS cc_start: 0.8960 (tttt) cc_final: 0.8702 (tttp) REVERT: B 291 LYS cc_start: 0.8877 (tttt) cc_final: 0.8501 (tttp) REVERT: B 312 ASP cc_start: 0.7717 (t0) cc_final: 0.7177 (t0) REVERT: B 321 LYS cc_start: 0.8675 (mttt) cc_final: 0.8365 (mtpp) REVERT: B 324 MET cc_start: 0.8374 (mmm) cc_final: 0.8079 (tpp) REVERT: B 329 GLU cc_start: 0.8341 (tt0) cc_final: 0.7194 (tm-30) REVERT: D 115 GLN cc_start: 0.8667 (tp40) cc_final: 0.8434 (tp40) REVERT: E 13 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8392 (pm20) REVERT: E 27 GLN cc_start: 0.8613 (mt0) cc_final: 0.8277 (mt0) REVERT: F 13 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8269 (pm20) REVERT: H 56 MET cc_start: 0.8913 (ttp) cc_final: 0.8663 (ttt) REVERT: J 36 TYR cc_start: 0.8481 (t80) cc_final: 0.8259 (t80) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.2273 time to fit residues: 66.8285 Evaluate side-chains 185 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0060 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 150 HIS A 163 ASN B 84 GLN B 145 GLN B 150 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 HIS J 24 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8435 Z= 0.179 Angle : 0.678 8.209 11487 Z= 0.325 Chirality : 0.042 0.170 1321 Planarity : 0.004 0.040 1412 Dihedral : 12.115 100.150 1887 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.22 % Allowed : 11.19 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.10 (0.28), residues: 1008 helix: 2.66 (0.26), residues: 356 sheet: -0.15 (0.26), residues: 402 loop : -0.47 (0.45), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 195 HIS 0.002 0.000 HIS J 24 PHE 0.014 0.001 PHE A 135 TYR 0.018 0.002 TYR I 33 ARG 0.010 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 49 ARG cc_start: 0.8473 (ptt90) cc_final: 0.8175 (ptt-90) REVERT: A 215 LYS cc_start: 0.8910 (tttt) cc_final: 0.8679 (tttm) REVERT: A 321 LYS cc_start: 0.8660 (mttt) cc_final: 0.8398 (mtmm) REVERT: A 329 GLU cc_start: 0.8090 (tt0) cc_final: 0.7110 (tm-30) REVERT: A 346 ASN cc_start: 0.8960 (t0) cc_final: 0.8735 (t0) REVERT: B 215 LYS cc_start: 0.8995 (tttt) cc_final: 0.8787 (tttm) REVERT: B 291 LYS cc_start: 0.8812 (tttt) cc_final: 0.8537 (tttp) REVERT: B 321 LYS cc_start: 0.8739 (mttt) cc_final: 0.8415 (mtpp) REVERT: B 329 GLU cc_start: 0.8159 (tt0) cc_final: 0.7408 (tm-30) REVERT: E 13 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8354 (pm20) REVERT: E 27 GLN cc_start: 0.8340 (mt0) cc_final: 0.7744 (mp10) REVERT: F 13 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8214 (pm20) REVERT: F 23 THR cc_start: 0.8762 (t) cc_final: 0.8163 (t) REVERT: F 27 GLN cc_start: 0.8369 (mt0) cc_final: 0.7828 (mp10) REVERT: H 56 MET cc_start: 0.9020 (ttp) cc_final: 0.8769 (ttt) REVERT: I 6 GLU cc_start: 0.8444 (pm20) cc_final: 0.7393 (pm20) REVERT: J 6 GLU cc_start: 0.8041 (pm20) cc_final: 0.6963 (pm20) outliers start: 10 outliers final: 6 residues processed: 179 average time/residue: 0.2210 time to fit residues: 52.6232 Evaluate side-chains 166 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8435 Z= 0.327 Angle : 0.676 7.776 11487 Z= 0.329 Chirality : 0.042 0.145 1321 Planarity : 0.004 0.029 1412 Dihedral : 10.920 93.235 1887 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.68 % Allowed : 12.17 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.07 (0.28), residues: 1008 helix: 2.79 (0.26), residues: 356 sheet: -0.22 (0.26), residues: 402 loop : -0.63 (0.45), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 236 HIS 0.002 0.001 HIS J 24 PHE 0.013 0.002 PHE A 135 TYR 0.021 0.002 TYR J 36 ARG 0.006 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 0.958 Fit side-chains REVERT: A 45 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 215 LYS cc_start: 0.8964 (tttt) cc_final: 0.8711 (tttm) REVERT: A 321 LYS cc_start: 0.8616 (mttt) cc_final: 0.8296 (mtpp) REVERT: A 329 GLU cc_start: 0.8209 (tt0) cc_final: 0.7209 (tm-30) REVERT: B 215 LYS cc_start: 0.9028 (tttt) cc_final: 0.8815 (tttm) REVERT: B 291 LYS cc_start: 0.8723 (tttt) cc_final: 0.8255 (tttp) REVERT: B 312 ASP cc_start: 0.7654 (t0) cc_final: 0.7245 (t70) REVERT: B 321 LYS cc_start: 0.8720 (mttt) cc_final: 0.8407 (mtpp) REVERT: B 329 GLU cc_start: 0.8231 (tt0) cc_final: 0.7445 (tm-30) REVERT: E 23 THR cc_start: 0.8744 (t) cc_final: 0.8276 (t) REVERT: E 24 PHE cc_start: 0.8557 (t80) cc_final: 0.8343 (t80) REVERT: E 27 GLN cc_start: 0.8414 (mt0) cc_final: 0.7778 (mp10) REVERT: F 23 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8209 (t) REVERT: F 27 GLN cc_start: 0.8380 (mt0) cc_final: 0.7839 (mp10) REVERT: H 56 MET cc_start: 0.9013 (ttp) cc_final: 0.8779 (ttt) outliers start: 22 outliers final: 12 residues processed: 167 average time/residue: 0.2153 time to fit residues: 48.2883 Evaluate side-chains 171 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8435 Z= 0.243 Angle : 0.641 7.162 11487 Z= 0.311 Chirality : 0.040 0.161 1321 Planarity : 0.004 0.037 1412 Dihedral : 10.396 93.478 1887 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.68 % Allowed : 13.50 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.13 (0.28), residues: 1008 helix: 2.91 (0.26), residues: 350 sheet: -0.23 (0.25), residues: 412 loop : -0.55 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.001 0.000 HIS J 24 PHE 0.012 0.001 PHE A 135 TYR 0.019 0.002 TYR D 68 ARG 0.011 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8102 (tm-30) REVERT: A 215 LYS cc_start: 0.8985 (tttt) cc_final: 0.8704 (tttm) REVERT: A 321 LYS cc_start: 0.8597 (mttt) cc_final: 0.8294 (mtpp) REVERT: A 329 GLU cc_start: 0.8183 (tt0) cc_final: 0.7203 (tm-30) REVERT: B 71 LYS cc_start: 0.8522 (tttp) cc_final: 0.8139 (ttmm) REVERT: B 215 LYS cc_start: 0.9020 (tttt) cc_final: 0.8784 (tttm) REVERT: B 291 LYS cc_start: 0.8669 (tttt) cc_final: 0.8198 (tttp) REVERT: B 312 ASP cc_start: 0.7678 (t0) cc_final: 0.7247 (t70) REVERT: B 321 LYS cc_start: 0.8705 (mttt) cc_final: 0.8398 (mtpp) REVERT: B 329 GLU cc_start: 0.8176 (tt0) cc_final: 0.7411 (tm-30) REVERT: C 115 GLN cc_start: 0.8892 (tp40) cc_final: 0.8612 (tp40) REVERT: E 23 THR cc_start: 0.8738 (t) cc_final: 0.8103 (t) REVERT: E 24 PHE cc_start: 0.8576 (t80) cc_final: 0.8364 (t80) REVERT: E 27 GLN cc_start: 0.8405 (mt0) cc_final: 0.7833 (mp10) REVERT: F 23 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8217 (t) REVERT: F 27 GLN cc_start: 0.8378 (mt0) cc_final: 0.7840 (mp10) REVERT: H 56 MET cc_start: 0.8981 (ttp) cc_final: 0.8758 (ttt) REVERT: J 42 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8223 (mmm-85) outliers start: 22 outliers final: 16 residues processed: 172 average time/residue: 0.2081 time to fit residues: 48.6117 Evaluate side-chains 176 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8435 Z= 0.330 Angle : 0.642 6.810 11487 Z= 0.315 Chirality : 0.041 0.174 1321 Planarity : 0.004 0.034 1412 Dihedral : 10.369 104.271 1887 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.80 % Allowed : 13.87 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.13 (0.28), residues: 1008 helix: 2.97 (0.26), residues: 348 sheet: -0.26 (0.26), residues: 412 loop : -0.54 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.002 0.001 HIS J 24 PHE 0.013 0.001 PHE A 135 TYR 0.020 0.002 TYR C 68 ARG 0.005 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 215 LYS cc_start: 0.8993 (tttt) cc_final: 0.8707 (tttm) REVERT: A 321 LYS cc_start: 0.8611 (mttt) cc_final: 0.8296 (mtpp) REVERT: A 329 GLU cc_start: 0.8229 (tt0) cc_final: 0.7259 (tm-30) REVERT: B 45 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 71 LYS cc_start: 0.8524 (tttp) cc_final: 0.8125 (ttmm) REVERT: B 215 LYS cc_start: 0.9027 (tttt) cc_final: 0.8783 (tttm) REVERT: B 321 LYS cc_start: 0.8712 (mttt) cc_final: 0.8377 (mtpp) REVERT: B 329 GLU cc_start: 0.8227 (tt0) cc_final: 0.7434 (tm-30) REVERT: C 115 GLN cc_start: 0.8867 (tp40) cc_final: 0.8618 (tp40) REVERT: E 23 THR cc_start: 0.8755 (t) cc_final: 0.8126 (t) REVERT: E 27 GLN cc_start: 0.8450 (mt0) cc_final: 0.7871 (mp10) REVERT: F 27 GLN cc_start: 0.8409 (mt0) cc_final: 0.7875 (mp10) REVERT: H 56 MET cc_start: 0.8989 (ttp) cc_final: 0.8746 (ttt) REVERT: I 42 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.8371 (mmm-85) REVERT: J 42 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8260 (mmm-85) outliers start: 23 outliers final: 21 residues processed: 171 average time/residue: 0.2084 time to fit residues: 48.7327 Evaluate side-chains 175 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8435 Z= 0.211 Angle : 0.607 7.313 11487 Z= 0.298 Chirality : 0.040 0.141 1321 Planarity : 0.003 0.030 1412 Dihedral : 10.175 109.855 1887 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.43 % Allowed : 15.09 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.17 (0.28), residues: 1008 helix: 2.96 (0.26), residues: 350 sheet: -0.25 (0.25), residues: 416 loop : -0.45 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.001 0.000 HIS A 83 PHE 0.011 0.001 PHE A 135 TYR 0.018 0.001 TYR C 68 ARG 0.004 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.814 Fit side-chains REVERT: A 45 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 215 LYS cc_start: 0.8991 (tttt) cc_final: 0.8721 (tttm) REVERT: A 321 LYS cc_start: 0.8602 (mttt) cc_final: 0.8286 (mtpp) REVERT: A 329 GLU cc_start: 0.8191 (tt0) cc_final: 0.7204 (tm-30) REVERT: B 45 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 215 LYS cc_start: 0.9008 (tttt) cc_final: 0.8784 (tttm) REVERT: B 321 LYS cc_start: 0.8669 (mttt) cc_final: 0.8347 (mtpp) REVERT: B 329 GLU cc_start: 0.8173 (tt0) cc_final: 0.7406 (tm-30) REVERT: E 23 THR cc_start: 0.8749 (t) cc_final: 0.8132 (t) REVERT: E 24 PHE cc_start: 0.8564 (t80) cc_final: 0.8333 (t80) REVERT: E 27 GLN cc_start: 0.8434 (mt0) cc_final: 0.7864 (mp10) REVERT: F 27 GLN cc_start: 0.8401 (mt0) cc_final: 0.7931 (mp10) REVERT: H 56 MET cc_start: 0.8981 (ttp) cc_final: 0.8747 (ttt) REVERT: I 42 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8414 (mmm-85) REVERT: J 42 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8331 (mmm-85) outliers start: 20 outliers final: 17 residues processed: 163 average time/residue: 0.1957 time to fit residues: 43.7655 Evaluate side-chains 163 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8435 Z= 0.221 Angle : 0.603 7.366 11487 Z= 0.296 Chirality : 0.040 0.169 1321 Planarity : 0.003 0.027 1412 Dihedral : 9.948 110.021 1887 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.55 % Allowed : 14.96 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.30 (0.28), residues: 1008 helix: 2.96 (0.26), residues: 350 sheet: -0.14 (0.25), residues: 410 loop : -0.28 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.001 0.000 HIS A 83 PHE 0.011 0.001 PHE A 135 TYR 0.021 0.001 TYR C 68 ARG 0.006 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 84 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: A 215 LYS cc_start: 0.8992 (tttt) cc_final: 0.8729 (tttm) REVERT: A 321 LYS cc_start: 0.8621 (mttt) cc_final: 0.8302 (mtpp) REVERT: A 329 GLU cc_start: 0.8193 (tt0) cc_final: 0.7207 (tm-30) REVERT: B 45 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 215 LYS cc_start: 0.9005 (tttt) cc_final: 0.8793 (tttm) REVERT: B 321 LYS cc_start: 0.8662 (mttt) cc_final: 0.8347 (mtpp) REVERT: B 329 GLU cc_start: 0.8173 (tt0) cc_final: 0.7412 (tm-30) REVERT: E 23 THR cc_start: 0.8751 (t) cc_final: 0.8142 (t) REVERT: E 24 PHE cc_start: 0.8581 (t80) cc_final: 0.8349 (t80) REVERT: E 27 GLN cc_start: 0.8431 (mt0) cc_final: 0.7881 (mp10) REVERT: F 27 GLN cc_start: 0.8405 (mt0) cc_final: 0.7938 (mp10) REVERT: H 56 MET cc_start: 0.8985 (ttp) cc_final: 0.8759 (ttt) REVERT: I 42 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8448 (mmm-85) REVERT: J 42 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8350 (mmm-85) outliers start: 21 outliers final: 18 residues processed: 160 average time/residue: 0.1986 time to fit residues: 43.6386 Evaluate side-chains 164 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 0.0030 chunk 8 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8435 Z= 0.171 Angle : 0.587 7.942 11487 Z= 0.290 Chirality : 0.039 0.157 1321 Planarity : 0.003 0.028 1412 Dihedral : 9.535 107.756 1887 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.19 % Allowed : 15.57 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.48 (0.28), residues: 1008 helix: 2.99 (0.26), residues: 350 sheet: 0.04 (0.25), residues: 410 loop : -0.18 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 195 HIS 0.001 0.000 HIS A 83 PHE 0.009 0.001 PHE A 135 TYR 0.021 0.001 TYR C 68 ARG 0.006 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.899 Fit side-chains REVERT: A 45 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 215 LYS cc_start: 0.8962 (tttt) cc_final: 0.8759 (tttm) REVERT: A 321 LYS cc_start: 0.8610 (mttt) cc_final: 0.8294 (mtpp) REVERT: A 329 GLU cc_start: 0.8133 (tt0) cc_final: 0.7210 (tm-30) REVERT: B 45 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8124 (tm-30) REVERT: B 215 LYS cc_start: 0.8987 (tttt) cc_final: 0.8770 (tttm) REVERT: B 321 LYS cc_start: 0.8691 (mttt) cc_final: 0.8364 (mtpp) REVERT: B 329 GLU cc_start: 0.8116 (tt0) cc_final: 0.7423 (tm-30) REVERT: E 23 THR cc_start: 0.8738 (t) cc_final: 0.8150 (t) REVERT: E 24 PHE cc_start: 0.8587 (t80) cc_final: 0.8352 (t80) REVERT: E 27 GLN cc_start: 0.8427 (mt0) cc_final: 0.7879 (mp10) REVERT: F 27 GLN cc_start: 0.8412 (mt0) cc_final: 0.7922 (mp10) REVERT: H 56 MET cc_start: 0.8977 (ttp) cc_final: 0.8774 (ttt) REVERT: I 42 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8553 (mmm-85) REVERT: J 42 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8429 (mmm-85) outliers start: 18 outliers final: 16 residues processed: 164 average time/residue: 0.1863 time to fit residues: 42.0855 Evaluate side-chains 163 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8435 Z= 0.256 Angle : 0.615 7.323 11487 Z= 0.306 Chirality : 0.040 0.178 1321 Planarity : 0.004 0.041 1412 Dihedral : 9.339 100.219 1887 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.19 % Allowed : 15.94 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.37 (0.28), residues: 1008 helix: 2.90 (0.26), residues: 350 sheet: -0.03 (0.25), residues: 410 loop : -0.21 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.001 0.000 HIS B 150 PHE 0.013 0.001 PHE A 135 TYR 0.020 0.002 TYR C 68 ARG 0.009 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 58 THR cc_start: 0.8668 (p) cc_final: 0.8447 (p) REVERT: A 215 LYS cc_start: 0.8988 (tttt) cc_final: 0.8772 (tttm) REVERT: A 321 LYS cc_start: 0.8605 (mttt) cc_final: 0.8276 (mtpp) REVERT: A 329 GLU cc_start: 0.8175 (tt0) cc_final: 0.7219 (tm-30) REVERT: B 45 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 215 LYS cc_start: 0.8997 (tttt) cc_final: 0.8781 (tttm) REVERT: B 321 LYS cc_start: 0.8687 (mttt) cc_final: 0.8338 (mtpp) REVERT: B 329 GLU cc_start: 0.8159 (tt0) cc_final: 0.7429 (tm-30) REVERT: E 23 THR cc_start: 0.8752 (t) cc_final: 0.8138 (t) REVERT: E 24 PHE cc_start: 0.8603 (t80) cc_final: 0.8359 (t80) REVERT: E 27 GLN cc_start: 0.8448 (mt0) cc_final: 0.7840 (mp10) REVERT: F 27 GLN cc_start: 0.8418 (mt0) cc_final: 0.7941 (mp10) REVERT: H 56 MET cc_start: 0.8993 (ttp) cc_final: 0.8774 (ttt) REVERT: I 42 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: J 42 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8437 (mmm-85) outliers start: 18 outliers final: 15 residues processed: 159 average time/residue: 0.2000 time to fit residues: 43.6009 Evaluate side-chains 163 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8435 Z= 0.269 Angle : 0.634 8.383 11487 Z= 0.317 Chirality : 0.040 0.160 1321 Planarity : 0.004 0.029 1412 Dihedral : 9.245 95.333 1887 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.70 % Allowed : 17.15 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.31 (0.28), residues: 1008 helix: 2.83 (0.26), residues: 350 sheet: -0.04 (0.25), residues: 410 loop : -0.26 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.001 0.000 HIS J 24 PHE 0.012 0.001 PHE A 135 TYR 0.020 0.001 TYR C 68 ARG 0.008 0.000 ARG D 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8077 (tm-30) REVERT: A 58 THR cc_start: 0.8633 (p) cc_final: 0.8405 (p) REVERT: A 215 LYS cc_start: 0.8983 (tttt) cc_final: 0.8763 (tttp) REVERT: A 287 ASP cc_start: 0.8686 (m-30) cc_final: 0.8300 (t0) REVERT: A 321 LYS cc_start: 0.8591 (mttt) cc_final: 0.8275 (mtpp) REVERT: A 329 GLU cc_start: 0.8198 (tt0) cc_final: 0.7232 (tm-30) REVERT: B 45 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 215 LYS cc_start: 0.8997 (tttt) cc_final: 0.8780 (tttm) REVERT: B 321 LYS cc_start: 0.8636 (mttt) cc_final: 0.8289 (mtpp) REVERT: B 329 GLU cc_start: 0.8180 (tt0) cc_final: 0.7421 (tm-30) REVERT: E 23 THR cc_start: 0.8753 (t) cc_final: 0.8128 (t) REVERT: E 24 PHE cc_start: 0.8607 (t80) cc_final: 0.8356 (t80) REVERT: E 27 GLN cc_start: 0.8402 (mt0) cc_final: 0.7862 (mp10) REVERT: F 27 GLN cc_start: 0.8424 (mt0) cc_final: 0.7960 (mp10) REVERT: H 56 MET cc_start: 0.8996 (ttp) cc_final: 0.8770 (ttt) REVERT: I 42 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8484 (mmm-85) REVERT: J 42 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8408 (mmm-85) outliers start: 14 outliers final: 14 residues processed: 156 average time/residue: 0.1932 time to fit residues: 41.3799 Evaluate side-chains 162 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079828 restraints weight = 45770.590| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 5.83 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 94 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 94 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8435 Z= 0.293 Angle : 0.639 7.612 11487 Z= 0.320 Chirality : 0.040 0.157 1321 Planarity : 0.004 0.028 1412 Dihedral : 9.158 87.481 1887 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.43 % Allowed : 16.42 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.26 (0.28), residues: 1008 helix: 2.82 (0.27), residues: 350 sheet: -0.02 (0.26), residues: 406 loop : -0.42 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.002 0.000 HIS J 24 PHE 0.012 0.001 PHE A 135 TYR 0.019 0.002 TYR C 68 ARG 0.009 0.000 ARG C 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.92 seconds wall clock time: 37 minutes 7.92 seconds (2227.92 seconds total)