Starting phenix.real_space_refine on Wed Feb 14 14:17:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vby_31885/02_2024/7vby_31885_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vby_31885/02_2024/7vby_31885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vby_31885/02_2024/7vby_31885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vby_31885/02_2024/7vby_31885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vby_31885/02_2024/7vby_31885_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vby_31885/02_2024/7vby_31885_trim_updated.pdb" } resolution = 2.54 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= 0.033 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 11 5.49 5 S 34 5.16 5 C 5431 2.51 5 N 1306 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ARG 173": "NH1" <-> "NH2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "I ARG 240": "NH1" <-> "NH2" Residue "I GLU 289": "OE1" <-> "OE2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "I ARG 348": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8207 Number of models: 1 Model: "" Number of chains: 19 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 463 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "J" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 184 Unusual residues: {'PC1': 3, 'UND': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PC1': 1, 'UND': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'UND': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'UND': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 195 Unusual residues: {'PC1': 3, 'UND': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'PC1': 1, 'UND': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'PC1': 2, 'UND': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'UND': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.58 Number of scatterers: 8207 At special positions: 0 Unit cell: (132.398, 110.472, 96.1362, 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 34 16.00 P 11 15.00 O 1425 8.00 N 1306 7.00 C 5431 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: 3.02 Conformation dependent library (CDL) restraints added in 1.3 seconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 2 sheets defined 33.8% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'B' and resid 88 through 91 No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 41 through 61 Processing helix chain 'D' and resid 14 through 47 Proline residue: D 42 - end of helix Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 41 through 61 Processing helix chain 'G' and resid 6 through 38 removed outlier: 3.633A pdb=" N GLN G 10 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 49 through 52 Processing helix chain 'E' and resid 16 through 47 Proline residue: E 42 - end of helix Processing helix chain 'I' and resid 88 through 91 No H-bonds generated for 'chain 'I' and resid 88 through 91' Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'H' and resid 64 through 95 removed outlier: 3.934A pdb=" N ASP H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 117 Processing helix chain 'C' and resid 63 through 95 Processing helix chain 'C' and resid 97 through 117 Processing helix chain 'J' and resid 7 through 24 removed outlier: 3.541A pdb=" N ARG J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 38 Processing helix chain 'J' and resid 49 through 52 Processing sheet with id= A, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.470A pdb=" N LEU B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLY B 100 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU B 358 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS B 102 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 160 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN B 181 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N PHE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 100 through 104 removed outlier: 4.469A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY I 269 " --> pdb=" O GLY I 266 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I 251 " --> pdb=" O GLY I 232 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU I 231 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER I 224 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY I 233 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU I 222 " --> pdb=" O GLY I 233 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU I 235 " --> pdb=" O HIS I 220 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N HIS I 220 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR I 237 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL I 218 " --> pdb=" O TYR I 237 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG I 239 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE I 216 " --> pdb=" O ARG I 239 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN I 179 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP I 188 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA I 177 " --> pdb=" O TRP I 188 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL I 190 " --> pdb=" O LYS I 175 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS I 175 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY I 192 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG I 173 " --> pdb=" O GLY I 192 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU I 160 " --> pdb=" O THR I 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE I 113 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL I 115 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY I 108 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N HIS I 117 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN I 106 " --> pdb=" O HIS I 117 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL I 119 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR I 104 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU I 121 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS I 102 " --> pdb=" O LEU I 121 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1434 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: 3.27 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: 1231 1.32 - 1.44: 2069 1.44 - 1.56: 4966 1.56 - 1.68: 22 1.68 - 1.81: 58 Bond restraints: 8346 Sorted by residual: bond pdb=" C PRO I 148 " pdb=" O PRO I 148 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.68e+00 bond pdb=" C PRO B 148 " pdb=" O PRO B 148 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.30e-02 5.92e+03 8.62e+00 bond pdb=" CA SER I 142 " pdb=" CB SER I 142 " ideal model delta sigma weight residual 1.536 1.502 0.034 1.25e-02 6.40e+03 7.36e+00 bond pdb=" N GLY I 245 " pdb=" CA GLY I 245 " ideal model delta sigma weight residual 1.446 1.471 -0.025 9.50e-03 1.11e+04 7.06e+00 bond pdb=" N SER I 142 " pdb=" CA SER I 142 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.11e-02 8.12e+03 6.39e+00 ... (remaining 8341 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 260 107.04 - 113.78: 4521 113.78 - 120.52: 3458 120.52 - 127.26: 2793 127.26 - 133.99: 80 Bond angle restraints: 11112 Sorted by residual: angle pdb=" CA PHE I 147 " pdb=" CB PHE I 147 " pdb=" CG PHE I 147 " ideal model delta sigma weight residual 113.80 107.66 6.14 1.00e+00 1.00e+00 3.77e+01 angle pdb=" CA PHE I 147 " pdb=" C PHE I 147 " pdb=" O PHE I 147 " ideal model delta sigma weight residual 120.16 112.22 7.94 1.37e+00 5.33e-01 3.36e+01 angle pdb=" N PHE I 147 " pdb=" CA PHE I 147 " pdb=" C PHE I 147 " ideal model delta sigma weight residual 109.81 122.43 -12.62 2.21e+00 2.05e-01 3.26e+01 angle pdb=" N PHE B 147 " pdb=" CA PHE B 147 " pdb=" C PHE B 147 " ideal model delta sigma weight residual 109.81 122.39 -12.58 2.21e+00 2.05e-01 3.24e+01 angle pdb=" CA PHE B 147 " pdb=" C PHE B 147 " pdb=" O PHE B 147 " ideal model delta sigma weight residual 120.16 112.54 7.62 1.37e+00 5.33e-01 3.09e+01 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4419 17.74 - 35.47: 532 35.47 - 53.21: 141 53.21 - 70.95: 41 70.95 - 88.68: 16 Dihedral angle restraints: 5149 sinusoidal: 2448 harmonic: 2701 Sorted by residual: dihedral pdb=" C PHE I 147 " pdb=" N PHE I 147 " pdb=" CA PHE I 147 " pdb=" CB PHE I 147 " ideal model delta harmonic sigma weight residual -122.60 -162.75 40.15 0 2.50e+00 1.60e-01 2.58e+02 dihedral pdb=" N PHE I 147 " pdb=" C PHE I 147 " pdb=" CA PHE I 147 " pdb=" CB PHE I 147 " ideal model delta harmonic sigma weight residual 122.80 161.93 -39.13 0 2.50e+00 1.60e-01 2.45e+02 dihedral pdb=" C PHE B 147 " pdb=" N PHE B 147 " pdb=" CA PHE B 147 " pdb=" CB PHE B 147 " ideal model delta harmonic sigma weight residual -122.60 -159.55 36.95 0 2.50e+00 1.60e-01 2.18e+02 ... (remaining 5146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 1164 0.347 - 0.695: 0 0.695 - 1.042: 0 1.042 - 1.389: 0 1.389 - 1.736: 2 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA PHE I 147 " pdb=" N PHE I 147 " pdb=" C PHE I 147 " pdb=" CB PHE I 147 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.54e+01 chirality pdb=" CA PHE B 147 " pdb=" N PHE B 147 " pdb=" C PHE B 147 " pdb=" CB PHE B 147 " both_signs ideal model delta sigma weight residual False 2.51 0.92 1.59 2.00e-01 2.50e+01 6.35e+01 chirality pdb=" CA LEU I 141 " pdb=" N LEU I 141 " pdb=" C LEU I 141 " pdb=" CB LEU I 141 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1163 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 147 " -0.025 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE I 147 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 147 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE I 147 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 147 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 147 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 147 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 147 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C PHE I 147 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE I 147 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO I 148 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 147 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C PHE B 147 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE B 147 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 148 " -0.013 2.00e-02 2.50e+03 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 139 2.68 - 3.23: 7427 3.23 - 3.79: 12044 3.79 - 4.34: 16368 4.34 - 4.90: 28488 Nonbonded interactions: 64466 Sorted by model distance: nonbonded pdb=" O GLN B 182 " pdb=" OG SER B 183 " model vdw 2.120 2.440 nonbonded pdb=" OE1 GLN B 167 " pdb=" NE ARG B 173 " model vdw 2.196 2.520 nonbonded pdb=" NE2 GLN B 223 " pdb=" O LEU E 38 " model vdw 2.250 2.520 nonbonded pdb=" O SER J 5 " pdb=" NZ LYS J 9 " model vdw 2.254 2.520 nonbonded pdb=" O GLN H 112 " pdb=" OE1 GLN H 116 " model vdw 2.278 3.040 ... (remaining 64461 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 67) selection = (chain 'F' and resid 25 through 67) } ncs_group { reference = chain 'B' selection = (chain 'I' and (resid 76 through 361 or resid 901 through 905)) } ncs_group { reference = (chain 'C' and (resid 63 through 118 or resid 201)) selection = (chain 'H' and (resid 63 through 118 or resid 201)) } ncs_group { reference = (chain 'D' and resid 13 through 48) selection = chain 'E' } ncs_group { reference = (chain 'G' and (resid 2 through 55 or resid 101)) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 7.040 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.890 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.007 0.051 8346 Z= 0.450 Angle : 0.846 12.624 11112 Z= 0.449 Chirality : 0.081 1.736 1166 Planarity : 0.004 0.049 1337 Dihedral : 16.966 88.683 3415 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.26 % Favored : 97.53 % Rotamer: Outliers : 0.75 % Allowed : 0.87 % Favored : 98.38 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.29), residues: 931 helix: 3.40 (0.29), residues: 325 sheet: 0.27 (0.26), residues: 382 loop : -1.18 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 86 HIS 0.006 0.001 HIS I 271 PHE 0.035 0.001 PHE I 147 TYR 0.007 0.001 TYR D 34 ARG 0.016 0.001 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 230 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: B 88 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8398 (ttm170) REVERT: B 176 MET cc_start: 0.8072 (mtm) cc_final: 0.7786 (mtm) REVERT: A 37 ASP cc_start: 0.9009 (t0) cc_final: 0.8723 (t0) REVERT: D 13 PRO cc_start: 0.9451 (Cg_exo) cc_final: 0.9156 (Cg_endo) REVERT: D 19 LYS cc_start: 0.9259 (tppp) cc_final: 0.8744 (tppp) REVERT: D 23 ASP cc_start: 0.8711 (m-30) cc_final: 0.8417 (m-30) REVERT: F 40 ASP cc_start: 0.8529 (t70) cc_final: 0.8230 (t0) REVERT: G 10 GLN cc_start: 0.8735 (mp10) cc_final: 0.8219 (pm20) REVERT: E 19 LYS cc_start: 0.9340 (tppp) cc_final: 0.8374 (tppp) REVERT: E 23 ASP cc_start: 0.8830 (m-30) cc_final: 0.7984 (m-30) REVERT: I 176 MET cc_start: 0.8018 (mtm) cc_final: 0.7771 (mtm) REVERT: H 67 PHE cc_start: 0.8797 (t80) cc_final: 0.8449 (t80) REVERT: H 75 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8298 (tm-30) REVERT: H 76 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8526 (mmmt) REVERT: H 104 GLU cc_start: 0.8746 (tp30) cc_final: 0.8524 (mm-30) REVERT: H 111 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 75 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7602 (tm-30) REVERT: C 104 GLU cc_start: 0.8722 (tp30) cc_final: 0.8506 (mm-30) REVERT: J 14 GLN cc_start: 0.8975 (mt0) cc_final: 0.8570 (mt0) REVERT: J 15 LEU cc_start: 0.9331 (tp) cc_final: 0.9064 (tt) REVERT: J 41 ASP cc_start: 0.8707 (m-30) cc_final: 0.8470 (m-30) outliers start: 6 outliers final: 3 residues processed: 235 average time/residue: 1.3555 time to fit residues: 335.4665 Evaluate side-chains 209 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS A 48 ASN F 39 ASN G 20 GLN I 106 ASN I 271 HIS H 115 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8346 Z= 0.247 Angle : 0.687 11.512 11112 Z= 0.342 Chirality : 0.046 0.455 1166 Planarity : 0.005 0.046 1337 Dihedral : 16.295 110.155 1643 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.35 % Allowed : 13.43 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.30), residues: 931 helix: 3.52 (0.28), residues: 319 sheet: 0.46 (0.26), residues: 386 loop : -0.88 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.006 0.001 HIS I 271 PHE 0.046 0.002 PHE B 147 TYR 0.009 0.001 TYR C 78 ARG 0.013 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8087 (mtm) cc_final: 0.7824 (mtm) REVERT: B 319 ASP cc_start: 0.8406 (t0) cc_final: 0.8158 (t0) REVERT: B 329 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 33 ARG cc_start: 0.8492 (mpt180) cc_final: 0.8105 (ptt-90) REVERT: A 37 ASP cc_start: 0.9118 (t0) cc_final: 0.8800 (t0) REVERT: D 18 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8029 (ttp80) REVERT: D 19 LYS cc_start: 0.9246 (tppp) cc_final: 0.8668 (tppp) REVERT: D 22 GLU cc_start: 0.8411 (pm20) cc_final: 0.7934 (pm20) REVERT: D 23 ASP cc_start: 0.8802 (m-30) cc_final: 0.8408 (m-30) REVERT: D 38 LEU cc_start: 0.8991 (mp) cc_final: 0.8584 (mp) REVERT: F 40 ASP cc_start: 0.8597 (t70) cc_final: 0.8248 (t0) REVERT: G 46 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: E 15 GLU cc_start: 0.7714 (tp30) cc_final: 0.7505 (tp30) REVERT: E 19 LYS cc_start: 0.9230 (tppp) cc_final: 0.8685 (tppp) REVERT: E 22 GLU cc_start: 0.8147 (pp20) cc_final: 0.7442 (pp20) REVERT: E 23 ASP cc_start: 0.8894 (m-30) cc_final: 0.8305 (m-30) REVERT: I 176 MET cc_start: 0.7983 (mtm) cc_final: 0.7737 (mtm) REVERT: I 293 ARG cc_start: 0.8821 (mtp-110) cc_final: 0.8614 (ttm110) REVERT: H 67 PHE cc_start: 0.8802 (t80) cc_final: 0.8438 (t80) REVERT: H 75 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8327 (tm-30) REVERT: H 76 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8519 (mmmt) REVERT: H 104 GLU cc_start: 0.8688 (tp30) cc_final: 0.8461 (mm-30) REVERT: H 107 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7967 (tm-30) REVERT: H 110 GLN cc_start: 0.8625 (pp30) cc_final: 0.8390 (pp30) REVERT: H 111 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8512 (pp30) REVERT: C 75 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7591 (tm-30) REVERT: C 76 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8466 (mmmt) REVERT: C 104 GLU cc_start: 0.8698 (tp30) cc_final: 0.8467 (mm-30) REVERT: C 107 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 110 GLN cc_start: 0.8579 (pp30) cc_final: 0.8364 (pp30) REVERT: J 9 LYS cc_start: 0.8972 (mptt) cc_final: 0.8675 (mptt) REVERT: J 13 GLN cc_start: 0.8527 (mt0) cc_final: 0.8074 (mt0) REVERT: J 46 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6360 (tp30) outliers start: 35 outliers final: 14 residues processed: 228 average time/residue: 1.2193 time to fit residues: 294.1421 Evaluate side-chains 218 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8346 Z= 0.263 Angle : 0.657 10.179 11112 Z= 0.325 Chirality : 0.044 0.365 1166 Planarity : 0.004 0.045 1337 Dihedral : 15.605 83.428 1637 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.35 % Allowed : 15.55 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.29), residues: 931 helix: 3.43 (0.28), residues: 319 sheet: 0.63 (0.26), residues: 386 loop : -0.93 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 25 HIS 0.003 0.001 HIS I 271 PHE 0.027 0.001 PHE B 147 TYR 0.008 0.001 TYR C 78 ARG 0.013 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8066 (mtm) cc_final: 0.7803 (mtm) REVERT: B 293 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8254 (mtp-110) REVERT: B 319 ASP cc_start: 0.8446 (t0) cc_final: 0.8160 (t0) REVERT: B 329 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: A 33 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8079 (ptt-90) REVERT: A 37 ASP cc_start: 0.9184 (t0) cc_final: 0.8868 (t0) REVERT: D 15 GLU cc_start: 0.8790 (pm20) cc_final: 0.7859 (pm20) REVERT: D 19 LYS cc_start: 0.9253 (tppp) cc_final: 0.8664 (tppp) REVERT: D 20 MET cc_start: 0.8670 (mtp) cc_final: 0.8328 (mtp) REVERT: D 23 ASP cc_start: 0.8765 (m-30) cc_final: 0.8316 (m-30) REVERT: D 29 ARG cc_start: 0.8906 (ttp-110) cc_final: 0.8654 (ttp80) REVERT: F 40 ASP cc_start: 0.8492 (t70) cc_final: 0.8170 (t0) REVERT: G 10 GLN cc_start: 0.8648 (mp10) cc_final: 0.8245 (pm20) REVERT: G 13 GLN cc_start: 0.7940 (mt0) cc_final: 0.7645 (mt0) REVERT: G 14 GLN cc_start: 0.8905 (mt0) cc_final: 0.8330 (mm-40) REVERT: G 46 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6110 (tp30) REVERT: E 19 LYS cc_start: 0.9241 (tppp) cc_final: 0.8695 (tppp) REVERT: E 22 GLU cc_start: 0.8225 (pp20) cc_final: 0.7703 (pp20) REVERT: E 23 ASP cc_start: 0.8922 (m-30) cc_final: 0.8400 (m-30) REVERT: E 38 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8632 (mp) REVERT: I 96 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9191 (pp) REVERT: I 147 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6513 (t80) REVERT: I 173 ARG cc_start: 0.8430 (ttm170) cc_final: 0.7854 (ttm170) REVERT: I 176 MET cc_start: 0.8008 (mtm) cc_final: 0.7772 (mtm) REVERT: H 67 PHE cc_start: 0.8807 (t80) cc_final: 0.8421 (t80) REVERT: H 72 PHE cc_start: 0.8969 (t80) cc_final: 0.8748 (t80) REVERT: H 75 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8343 (tm-30) REVERT: H 76 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8494 (mmmt) REVERT: H 104 GLU cc_start: 0.8664 (tp30) cc_final: 0.8445 (mm-30) REVERT: H 107 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8023 (tm-30) REVERT: H 111 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8478 (pp30) REVERT: C 75 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7708 (tm-30) REVERT: C 76 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8424 (mmmt) REVERT: C 104 GLU cc_start: 0.8669 (tp30) cc_final: 0.8454 (mm-30) REVERT: C 107 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 110 GLN cc_start: 0.8514 (pp30) cc_final: 0.8291 (pp30) REVERT: J 46 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6409 (tp30) outliers start: 35 outliers final: 17 residues processed: 224 average time/residue: 1.2240 time to fit residues: 290.1234 Evaluate side-chains 227 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN F 39 ASN I 79 ASN I 111 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8346 Z= 0.245 Angle : 0.649 9.644 11112 Z= 0.320 Chirality : 0.043 0.329 1166 Planarity : 0.004 0.046 1337 Dihedral : 15.265 84.378 1637 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.60 % Allowed : 17.16 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.29), residues: 931 helix: 3.46 (0.29), residues: 319 sheet: 0.75 (0.26), residues: 386 loop : -0.85 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 25 HIS 0.002 0.001 HIS I 271 PHE 0.022 0.001 PHE I 147 TYR 0.007 0.001 TYR C 78 ARG 0.014 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9176 (pp) REVERT: B 176 MET cc_start: 0.8047 (mtm) cc_final: 0.7783 (mtm) REVERT: B 319 ASP cc_start: 0.8453 (t0) cc_final: 0.8140 (t0) REVERT: A 33 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8064 (ptt-90) REVERT: A 37 ASP cc_start: 0.9262 (t0) cc_final: 0.8888 (t0) REVERT: D 19 LYS cc_start: 0.9215 (tppp) cc_final: 0.8515 (tppp) REVERT: D 20 MET cc_start: 0.8726 (mtp) cc_final: 0.8412 (mtt) REVERT: D 23 ASP cc_start: 0.8736 (m-30) cc_final: 0.8199 (m-30) REVERT: D 29 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.8652 (ttp80) REVERT: F 40 ASP cc_start: 0.8489 (t70) cc_final: 0.8167 (t0) REVERT: G 13 GLN cc_start: 0.7959 (mt0) cc_final: 0.7663 (mt0) REVERT: G 14 GLN cc_start: 0.8889 (mt0) cc_final: 0.8328 (mm-40) REVERT: G 46 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6085 (tp30) REVERT: E 15 GLU cc_start: 0.7552 (tp30) cc_final: 0.7191 (tp30) REVERT: E 19 LYS cc_start: 0.9223 (tppp) cc_final: 0.8506 (tppp) REVERT: E 22 GLU cc_start: 0.8271 (pp20) cc_final: 0.7879 (pp20) REVERT: E 23 ASP cc_start: 0.8911 (m-30) cc_final: 0.8357 (m-30) REVERT: E 38 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8686 (mp) REVERT: I 96 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9194 (pp) REVERT: I 147 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: I 173 ARG cc_start: 0.8386 (ttm170) cc_final: 0.8020 (ttm170) REVERT: I 176 MET cc_start: 0.8006 (mtm) cc_final: 0.7772 (mtm) REVERT: I 294 MET cc_start: 0.8788 (mpm) cc_final: 0.8538 (mmp) REVERT: H 67 PHE cc_start: 0.8807 (t80) cc_final: 0.8418 (t80) REVERT: H 72 PHE cc_start: 0.8953 (t80) cc_final: 0.8736 (t80) REVERT: H 75 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8363 (tm-30) REVERT: H 76 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8478 (mmmt) REVERT: H 104 GLU cc_start: 0.8661 (tp30) cc_final: 0.8438 (mm-30) REVERT: H 107 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8041 (tm-30) REVERT: H 111 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8522 (tm-30) REVERT: H 115 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8565 (mm-40) REVERT: C 75 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7736 (tm-30) REVERT: C 76 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8392 (mmmt) REVERT: C 104 GLU cc_start: 0.8648 (tp30) cc_final: 0.8431 (mm-30) REVERT: C 107 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 110 GLN cc_start: 0.8482 (pp30) cc_final: 0.8263 (pp30) REVERT: J 14 GLN cc_start: 0.8949 (mt0) cc_final: 0.8547 (mt0) outliers start: 37 outliers final: 20 residues processed: 220 average time/residue: 1.2042 time to fit residues: 280.4293 Evaluate side-chains 233 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN F 39 ASN H 115 GLN C 111 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8346 Z= 0.290 Angle : 0.671 9.377 11112 Z= 0.330 Chirality : 0.043 0.310 1166 Planarity : 0.005 0.055 1337 Dihedral : 15.115 84.396 1637 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.73 % Allowed : 17.91 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.29), residues: 931 helix: 3.39 (0.29), residues: 319 sheet: 0.75 (0.26), residues: 388 loop : -0.74 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 25 HIS 0.003 0.001 HIS I 271 PHE 0.021 0.001 PHE I 147 TYR 0.008 0.001 TYR D 34 ARG 0.016 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 213 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: B 176 MET cc_start: 0.8044 (mtm) cc_final: 0.7772 (mtm) REVERT: B 294 MET cc_start: 0.8823 (mmm) cc_final: 0.8529 (mpm) REVERT: B 319 ASP cc_start: 0.8529 (t0) cc_final: 0.8186 (t0) REVERT: A 33 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8093 (ptt-90) REVERT: A 37 ASP cc_start: 0.9270 (t0) cc_final: 0.8876 (t0) REVERT: D 15 GLU cc_start: 0.8626 (pm20) cc_final: 0.8413 (pm20) REVERT: D 16 MET cc_start: 0.8167 (mpt) cc_final: 0.7951 (mpt) REVERT: D 19 LYS cc_start: 0.9164 (tppp) cc_final: 0.8398 (tppp) REVERT: D 20 MET cc_start: 0.8694 (mtp) cc_final: 0.8419 (mtt) REVERT: D 22 GLU cc_start: 0.8417 (pp20) cc_final: 0.7495 (pp20) REVERT: D 23 ASP cc_start: 0.8720 (m-30) cc_final: 0.8184 (m-30) REVERT: D 29 ARG cc_start: 0.8896 (ttp-110) cc_final: 0.8648 (ttp80) REVERT: F 40 ASP cc_start: 0.8520 (t70) cc_final: 0.8193 (t0) REVERT: G 13 GLN cc_start: 0.8008 (mt0) cc_final: 0.7766 (mt0) REVERT: G 14 GLN cc_start: 0.8920 (mt0) cc_final: 0.8369 (mm110) REVERT: G 46 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5957 (tp30) REVERT: E 19 LYS cc_start: 0.9231 (tppp) cc_final: 0.8545 (tppp) REVERT: E 22 GLU cc_start: 0.8324 (pp20) cc_final: 0.7881 (pp20) REVERT: E 23 ASP cc_start: 0.8893 (m-30) cc_final: 0.8349 (m-30) REVERT: E 38 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8726 (mp) REVERT: I 96 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9201 (pp) REVERT: I 147 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6200 (m-80) REVERT: I 173 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8101 (ttm170) REVERT: I 176 MET cc_start: 0.8023 (mtm) cc_final: 0.7784 (mtm) REVERT: H 67 PHE cc_start: 0.8812 (t80) cc_final: 0.8416 (t80) REVERT: H 72 PHE cc_start: 0.8975 (t80) cc_final: 0.8751 (t80) REVERT: H 75 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8321 (tm-30) REVERT: H 76 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8456 (mmmt) REVERT: H 104 GLU cc_start: 0.8672 (tp30) cc_final: 0.8196 (tp30) REVERT: H 107 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8004 (tm-30) REVERT: H 111 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8451 (tm-30) REVERT: H 115 GLN cc_start: 0.8971 (mm110) cc_final: 0.8673 (mm-40) REVERT: C 75 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7675 (tm-30) REVERT: C 76 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8382 (mmmt) REVERT: C 104 GLU cc_start: 0.8642 (tp30) cc_final: 0.8201 (tp30) REVERT: C 107 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 110 GLN cc_start: 0.8473 (pp30) cc_final: 0.8200 (pp30) REVERT: J 10 GLN cc_start: 0.8892 (pm20) cc_final: 0.8655 (pm20) REVERT: J 13 GLN cc_start: 0.8551 (mt0) cc_final: 0.8281 (mt0) REVERT: J 14 GLN cc_start: 0.8957 (mt0) cc_final: 0.8606 (mt0) REVERT: J 46 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6178 (tp30) outliers start: 38 outliers final: 20 residues processed: 223 average time/residue: 1.2222 time to fit residues: 288.6262 Evaluate side-chains 236 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 9 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN F 39 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8346 Z= 0.177 Angle : 0.644 8.445 11112 Z= 0.318 Chirality : 0.042 0.241 1166 Planarity : 0.005 0.059 1337 Dihedral : 14.711 82.434 1637 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.10 % Allowed : 19.78 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.29), residues: 931 helix: 3.41 (0.29), residues: 319 sheet: 0.88 (0.26), residues: 388 loop : -0.62 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 86 HIS 0.002 0.001 HIS I 271 PHE 0.022 0.001 PHE C 67 TYR 0.007 0.001 TYR C 78 ARG 0.016 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8005 (mtm) cc_final: 0.7748 (mtm) REVERT: B 293 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8451 (ttp80) REVERT: B 319 ASP cc_start: 0.8445 (t0) cc_final: 0.8167 (t0) REVERT: A 37 ASP cc_start: 0.9295 (t0) cc_final: 0.8922 (t0) REVERT: D 19 LYS cc_start: 0.9212 (tppp) cc_final: 0.8500 (tppp) REVERT: D 20 MET cc_start: 0.8620 (mtp) cc_final: 0.8415 (mtt) REVERT: D 22 GLU cc_start: 0.8256 (pp20) cc_final: 0.7548 (pp20) REVERT: D 23 ASP cc_start: 0.8678 (m-30) cc_final: 0.8168 (m-30) REVERT: D 29 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8647 (ttp80) REVERT: F 33 ARG cc_start: 0.8495 (ptt180) cc_final: 0.8210 (ptp90) REVERT: F 40 ASP cc_start: 0.8457 (t70) cc_final: 0.8160 (t0) REVERT: G 13 GLN cc_start: 0.8026 (mt0) cc_final: 0.7735 (mt0) REVERT: G 14 GLN cc_start: 0.8898 (mt0) cc_final: 0.8339 (mm110) REVERT: E 19 LYS cc_start: 0.9167 (tppp) cc_final: 0.8633 (mttt) REVERT: E 23 ASP cc_start: 0.8880 (m-30) cc_final: 0.8412 (m-30) REVERT: I 173 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7820 (ttm170) REVERT: I 176 MET cc_start: 0.7992 (mtm) cc_final: 0.7767 (mtm) REVERT: H 67 PHE cc_start: 0.8813 (t80) cc_final: 0.8420 (t80) REVERT: H 72 PHE cc_start: 0.8957 (t80) cc_final: 0.8742 (t80) REVERT: H 75 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8390 (tm-30) REVERT: H 76 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8459 (mmmt) REVERT: H 104 GLU cc_start: 0.8665 (tp30) cc_final: 0.8157 (tp30) REVERT: H 107 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7975 (tm-30) REVERT: H 111 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8447 (tm-30) REVERT: H 115 GLN cc_start: 0.9006 (mm110) cc_final: 0.8735 (mm-40) REVERT: C 75 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7536 (tm-30) REVERT: C 76 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8386 (mmmt) REVERT: C 104 GLU cc_start: 0.8616 (tp30) cc_final: 0.8165 (tp30) REVERT: C 107 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 110 GLN cc_start: 0.8431 (pp30) cc_final: 0.8192 (pp30) REVERT: J 13 GLN cc_start: 0.8557 (mt0) cc_final: 0.8262 (mt0) REVERT: J 14 GLN cc_start: 0.8951 (mt0) cc_final: 0.8572 (mt0) REVERT: J 46 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6369 (tp30) outliers start: 33 outliers final: 19 residues processed: 229 average time/residue: 1.2285 time to fit residues: 297.5920 Evaluate side-chains 230 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8346 Z= 0.199 Angle : 0.665 8.774 11112 Z= 0.328 Chirality : 0.042 0.226 1166 Planarity : 0.005 0.062 1337 Dihedral : 14.527 81.862 1637 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.36 % Allowed : 20.90 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.29), residues: 931 helix: 3.38 (0.29), residues: 319 sheet: 1.01 (0.26), residues: 386 loop : -0.53 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 25 HIS 0.002 0.001 HIS I 271 PHE 0.022 0.001 PHE B 147 TYR 0.008 0.001 TYR E 34 ARG 0.017 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8002 (mtm) cc_final: 0.7795 (mtm) REVERT: B 293 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8387 (ttp80) REVERT: B 319 ASP cc_start: 0.8467 (t0) cc_final: 0.8180 (t0) REVERT: A 37 ASP cc_start: 0.9293 (t0) cc_final: 0.8947 (t0) REVERT: D 18 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8326 (ttp80) REVERT: D 19 LYS cc_start: 0.9237 (tppp) cc_final: 0.8527 (tppp) REVERT: D 20 MET cc_start: 0.8548 (mtp) cc_final: 0.8334 (mtm) REVERT: D 22 GLU cc_start: 0.8278 (pp20) cc_final: 0.7513 (pp20) REVERT: D 23 ASP cc_start: 0.8707 (m-30) cc_final: 0.8233 (m-30) REVERT: D 29 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8647 (ttp80) REVERT: F 33 ARG cc_start: 0.8442 (ptt180) cc_final: 0.8030 (ptt-90) REVERT: F 40 ASP cc_start: 0.8459 (t70) cc_final: 0.8158 (t0) REVERT: G 13 GLN cc_start: 0.8028 (mt0) cc_final: 0.7737 (mt0) REVERT: G 14 GLN cc_start: 0.8870 (mt0) cc_final: 0.8323 (mm110) REVERT: E 19 LYS cc_start: 0.8991 (tppp) cc_final: 0.8727 (mttm) REVERT: E 22 GLU cc_start: 0.8039 (pp20) cc_final: 0.7833 (pp20) REVERT: E 38 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8753 (mp) REVERT: I 96 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9213 (pp) REVERT: I 173 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7858 (ttm170) REVERT: I 176 MET cc_start: 0.8001 (mtm) cc_final: 0.7777 (mtm) REVERT: H 67 PHE cc_start: 0.8818 (t80) cc_final: 0.8425 (t80) REVERT: H 72 PHE cc_start: 0.8948 (t80) cc_final: 0.8744 (t80) REVERT: H 75 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8340 (tm-30) REVERT: H 76 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8455 (mmmt) REVERT: H 104 GLU cc_start: 0.8655 (tp30) cc_final: 0.8152 (tp30) REVERT: H 107 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7994 (tm-30) REVERT: H 111 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8460 (tm-30) REVERT: H 115 GLN cc_start: 0.9041 (mm110) cc_final: 0.8752 (mm-40) REVERT: C 75 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7677 (tm-30) REVERT: C 76 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8373 (mmmt) REVERT: C 104 GLU cc_start: 0.8621 (tp30) cc_final: 0.8185 (tp30) REVERT: C 107 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7975 (tm-30) REVERT: C 110 GLN cc_start: 0.8398 (pp30) cc_final: 0.8157 (pp30) REVERT: J 13 GLN cc_start: 0.8564 (mt0) cc_final: 0.8259 (mt0) REVERT: J 14 GLN cc_start: 0.8956 (mt0) cc_final: 0.8576 (mt0) REVERT: J 46 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6358 (tp30) outliers start: 27 outliers final: 17 residues processed: 215 average time/residue: 1.2448 time to fit residues: 282.8458 Evaluate side-chains 224 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8346 Z= 0.239 Angle : 0.695 9.802 11112 Z= 0.340 Chirality : 0.043 0.279 1166 Planarity : 0.005 0.075 1337 Dihedral : 14.502 82.274 1637 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.36 % Allowed : 21.77 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.29), residues: 931 helix: 3.38 (0.29), residues: 319 sheet: 0.99 (0.26), residues: 386 loop : -0.55 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 25 HIS 0.002 0.001 HIS I 271 PHE 0.025 0.001 PHE C 67 TYR 0.009 0.001 TYR E 34 ARG 0.018 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 176 MET cc_start: 0.8067 (mtm) cc_final: 0.7816 (mtm) REVERT: B 293 ARG cc_start: 0.8684 (ptm-80) cc_final: 0.8149 (ppp80) REVERT: B 319 ASP cc_start: 0.8507 (t0) cc_final: 0.8207 (t0) REVERT: A 33 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8053 (ptt-90) REVERT: A 37 ASP cc_start: 0.9305 (t0) cc_final: 0.8995 (t0) REVERT: D 18 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8333 (ttp80) REVERT: D 19 LYS cc_start: 0.9242 (tppp) cc_final: 0.8565 (tppp) REVERT: D 22 GLU cc_start: 0.8276 (pp20) cc_final: 0.7505 (pp20) REVERT: D 23 ASP cc_start: 0.8763 (m-30) cc_final: 0.8279 (m-30) REVERT: D 29 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8650 (ttp80) REVERT: F 40 ASP cc_start: 0.8482 (t70) cc_final: 0.8174 (t0) REVERT: G 13 GLN cc_start: 0.8040 (mt0) cc_final: 0.7721 (mt0) REVERT: G 14 GLN cc_start: 0.8892 (mt0) cc_final: 0.8327 (mm110) REVERT: G 46 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6057 (tp30) REVERT: E 19 LYS cc_start: 0.9066 (tppp) cc_final: 0.8754 (mttt) REVERT: E 38 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8745 (mp) REVERT: I 147 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.5821 (t80) REVERT: I 173 ARG cc_start: 0.8306 (ttm170) cc_final: 0.7910 (ttm170) REVERT: I 176 MET cc_start: 0.8018 (mtm) cc_final: 0.7796 (mtm) REVERT: H 67 PHE cc_start: 0.8818 (t80) cc_final: 0.8430 (t80) REVERT: H 72 PHE cc_start: 0.8958 (t80) cc_final: 0.8726 (t80) REVERT: H 75 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8365 (tm-30) REVERT: H 76 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8462 (mmmt) REVERT: H 104 GLU cc_start: 0.8665 (tp30) cc_final: 0.8174 (tp30) REVERT: H 107 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7965 (tm-30) REVERT: H 111 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 75 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7558 (tm-30) REVERT: C 76 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8366 (mmmt) REVERT: C 104 GLU cc_start: 0.8628 (tp30) cc_final: 0.8195 (tp30) REVERT: C 107 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 110 GLN cc_start: 0.8409 (pp30) cc_final: 0.8158 (pp30) REVERT: J 10 GLN cc_start: 0.8949 (pm20) cc_final: 0.8673 (pm20) REVERT: J 13 GLN cc_start: 0.8573 (mt0) cc_final: 0.8288 (mt0) REVERT: J 14 GLN cc_start: 0.8970 (mt0) cc_final: 0.8541 (mt0) REVERT: J 46 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6398 (tp30) outliers start: 27 outliers final: 13 residues processed: 218 average time/residue: 1.2912 time to fit residues: 297.9138 Evaluate side-chains 223 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8346 Z= 0.191 Angle : 0.702 10.386 11112 Z= 0.343 Chirality : 0.042 0.253 1166 Planarity : 0.005 0.070 1337 Dihedral : 14.311 81.629 1637 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.86 % Allowed : 22.64 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.29), residues: 931 helix: 3.30 (0.29), residues: 319 sheet: 1.04 (0.26), residues: 386 loop : -0.50 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 27 HIS 0.002 0.001 HIS I 117 PHE 0.021 0.001 PHE B 147 TYR 0.007 0.001 TYR E 34 ARG 0.019 0.001 ARG I 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8046 (mtm) cc_final: 0.7808 (mtm) REVERT: B 293 ARG cc_start: 0.8674 (ptm-80) cc_final: 0.8147 (ppp80) REVERT: B 319 ASP cc_start: 0.8425 (t0) cc_final: 0.8144 (t0) REVERT: A 33 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8071 (ptt-90) REVERT: A 37 ASP cc_start: 0.9307 (t0) cc_final: 0.9022 (t0) REVERT: D 19 LYS cc_start: 0.9226 (tppp) cc_final: 0.8550 (tppp) REVERT: D 22 GLU cc_start: 0.8266 (pp20) cc_final: 0.7488 (pp20) REVERT: D 23 ASP cc_start: 0.8756 (m-30) cc_final: 0.8235 (m-30) REVERT: D 29 ARG cc_start: 0.8861 (ttp-110) cc_final: 0.8631 (ttp80) REVERT: F 33 ARG cc_start: 0.8398 (ptt180) cc_final: 0.8158 (ptp90) REVERT: F 40 ASP cc_start: 0.8456 (t70) cc_final: 0.8151 (t0) REVERT: G 13 GLN cc_start: 0.8047 (mt0) cc_final: 0.7716 (mt0) REVERT: G 14 GLN cc_start: 0.8854 (mt0) cc_final: 0.8635 (mt0) REVERT: G 46 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6198 (tp30) REVERT: E 19 LYS cc_start: 0.9027 (tppp) cc_final: 0.8590 (tppp) REVERT: E 23 ASP cc_start: 0.8659 (m-30) cc_final: 0.8387 (m-30) REVERT: E 38 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8728 (mp) REVERT: I 176 MET cc_start: 0.7999 (mtm) cc_final: 0.7778 (mtm) REVERT: H 67 PHE cc_start: 0.8819 (t80) cc_final: 0.8435 (t80) REVERT: H 72 PHE cc_start: 0.8945 (t80) cc_final: 0.8730 (t80) REVERT: H 75 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8344 (tm-30) REVERT: H 76 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8455 (mmmt) REVERT: H 104 GLU cc_start: 0.8659 (tp30) cc_final: 0.8161 (tp30) REVERT: H 107 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8064 (tm-30) REVERT: H 111 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8618 (tm-30) REVERT: C 75 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7553 (tm-30) REVERT: C 76 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8386 (mmmt) REVERT: C 104 GLU cc_start: 0.8623 (tp30) cc_final: 0.8192 (tp30) REVERT: C 107 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8000 (tm-30) REVERT: C 110 GLN cc_start: 0.8386 (pp30) cc_final: 0.8150 (pp30) REVERT: C 115 GLN cc_start: 0.9429 (tm-30) cc_final: 0.9203 (pp30) REVERT: J 9 LYS cc_start: 0.8795 (mptt) cc_final: 0.8583 (mptt) REVERT: J 10 GLN cc_start: 0.8935 (pm20) cc_final: 0.8699 (pm20) REVERT: J 13 GLN cc_start: 0.8575 (mt0) cc_final: 0.8289 (mt0) REVERT: J 14 GLN cc_start: 0.8950 (mt0) cc_final: 0.8525 (mt0) REVERT: J 46 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6365 (tp30) outliers start: 23 outliers final: 16 residues processed: 219 average time/residue: 1.2458 time to fit residues: 288.2927 Evaluate side-chains 224 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8346 Z= 0.255 Angle : 0.752 10.753 11112 Z= 0.374 Chirality : 0.043 0.272 1166 Planarity : 0.006 0.081 1337 Dihedral : 14.320 81.738 1637 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.61 % Allowed : 22.76 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.20 (0.29), residues: 931 helix: 3.32 (0.29), residues: 317 sheet: 1.05 (0.26), residues: 386 loop : -0.56 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 25 HIS 0.002 0.001 HIS I 271 PHE 0.023 0.001 PHE I 147 TYR 0.009 0.001 TYR E 34 ARG 0.016 0.001 ARG D 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8070 (mtm) cc_final: 0.7822 (mtm) REVERT: B 293 ARG cc_start: 0.8673 (ptm-80) cc_final: 0.8134 (ppp80) REVERT: B 319 ASP cc_start: 0.8494 (t0) cc_final: 0.8202 (t0) REVERT: A 33 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (ptt-90) REVERT: A 37 ASP cc_start: 0.9300 (t0) cc_final: 0.9025 (t0) REVERT: D 19 LYS cc_start: 0.9202 (tppp) cc_final: 0.8760 (tppp) REVERT: D 22 GLU cc_start: 0.8262 (pp20) cc_final: 0.8004 (pp20) REVERT: D 29 ARG cc_start: 0.8869 (ttp-110) cc_final: 0.8642 (ttp80) REVERT: F 40 ASP cc_start: 0.8482 (t70) cc_final: 0.8163 (t0) REVERT: G 13 GLN cc_start: 0.8038 (mt0) cc_final: 0.7701 (mt0) REVERT: G 14 GLN cc_start: 0.8864 (mt0) cc_final: 0.8641 (mt0) REVERT: G 41 ASP cc_start: 0.7915 (m-30) cc_final: 0.7667 (m-30) REVERT: G 46 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6217 (tp30) REVERT: E 19 LYS cc_start: 0.8961 (tppp) cc_final: 0.8646 (tppp) REVERT: E 38 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8743 (mp) REVERT: I 176 MET cc_start: 0.8024 (mtm) cc_final: 0.7801 (mtm) REVERT: I 293 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8372 (ptm160) REVERT: H 67 PHE cc_start: 0.8825 (t80) cc_final: 0.8440 (t80) REVERT: H 72 PHE cc_start: 0.8958 (t80) cc_final: 0.8739 (t80) REVERT: H 75 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8354 (tm-30) REVERT: H 76 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8459 (mmmt) REVERT: H 104 GLU cc_start: 0.8678 (tp30) cc_final: 0.8208 (tp30) REVERT: H 107 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8068 (tm-30) REVERT: H 111 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 75 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7558 (tm-30) REVERT: C 76 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8350 (mmmt) REVERT: C 104 GLU cc_start: 0.8631 (tp30) cc_final: 0.8220 (tp30) REVERT: C 107 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 110 GLN cc_start: 0.8378 (pp30) cc_final: 0.8150 (pp30) REVERT: C 115 GLN cc_start: 0.9408 (tm-30) cc_final: 0.9181 (pp30) REVERT: J 9 LYS cc_start: 0.8807 (mptt) cc_final: 0.8587 (mptt) REVERT: J 10 GLN cc_start: 0.8926 (pm20) cc_final: 0.8699 (pm20) REVERT: J 13 GLN cc_start: 0.8580 (mt0) cc_final: 0.8286 (mt0) REVERT: J 14 GLN cc_start: 0.8954 (mt0) cc_final: 0.8530 (mt0) REVERT: J 44 MET cc_start: 0.8154 (mpp) cc_final: 0.7916 (pmm) REVERT: J 46 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6360 (tp30) outliers start: 21 outliers final: 16 residues processed: 214 average time/residue: 1.3299 time to fit residues: 300.7008 Evaluate side-chains 225 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN I 257 ASN I 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062912 restraints weight = 16048.071| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.67 r_work: 0.2746 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8346 Z= 0.186 Angle : 0.728 10.982 11112 Z= 0.363 Chirality : 0.042 0.244 1166 Planarity : 0.005 0.072 1337 Dihedral : 13.989 81.221 1637 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.36 % Allowed : 23.76 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.29), residues: 931 helix: 3.27 (0.29), residues: 317 sheet: 1.12 (0.27), residues: 386 loop : -0.51 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 86 HIS 0.002 0.000 HIS I 117 PHE 0.027 0.001 PHE C 67 TYR 0.007 0.001 TYR E 34 ARG 0.020 0.001 ARG B 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.90 seconds wall clock time: 81 minutes 16.91 seconds (4876.91 seconds total)