Starting phenix.real_space_refine on Tue Feb 13 17:00:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xxi_33504/02_2024/7xxi_33504_updated.pdb" } resolution = 3.0 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= 0.004 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 2 5.49 5 S 48 5.16 5 C 4499 2.51 5 N 1177 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7002 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2333 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 282} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1698 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2521 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 421 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'6AD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.59 Number of scatterers: 7002 At special positions: 0 Unit cell: (105.545, 114.95, 82.555, 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 48 16.00 P 2 15.00 O 1276 8.00 N 1177 7.00 C 4499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 8 sheets defined 42.3% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 23 through 52 Proline residue: A 29 - end of helix removed outlier: 4.288A pdb=" N PHE A 37 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 38 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN A 43 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A 50 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A 51 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 100 through 127 Processing helix chain 'A' and resid 135 through 161 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 181 through 223 Processing helix chain 'A' and resid 231 through 247 removed outlier: 3.884A pdb=" N ASN A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 removed outlier: 4.079A pdb=" N ILE A 257 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 271 through 301 removed outlier: 3.621A pdb=" N ASN A 274 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP A 294 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 295 - end of helix removed outlier: 3.735A pdb=" N LEU A 301 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'B' and resid 7 through 32 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.837A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 50' Processing helix chain 'B' and resid 213 through 216 removed outlier: 3.535A pdb=" N PHE B 216 " --> pdb=" O ILE B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 272 through 279 removed outlier: 4.201A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 309 removed outlier: 4.151A pdb=" N PHE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.547A pdb=" N VAL B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 36 removed outlier: 4.159A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.334A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.594A pdb=" N ILE B 265 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS B 323 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 267 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.042A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.012A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 148 through 153 removed outlier: 6.505A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 208 through 212 removed outlier: 3.642A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.608A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.576A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 317 through 320 removed outlier: 3.711A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 888 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: 1.88 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2226 1.35 - 1.47: 1828 1.47 - 1.60: 3025 1.60 - 1.72: 4 1.72 - 1.85: 67 Bond restraints: 7150 Sorted by residual: bond pdb=" C3' 6AD A 401 " pdb=" C4' 6AD A 401 " ideal model delta sigma weight residual 1.267 1.574 -0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C4' 6AD A 401 " pdb=" O4' 6AD A 401 " ideal model delta sigma weight residual 1.558 1.316 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C2' 6AD A 401 " pdb=" C3' 6AD A 401 " ideal model delta sigma weight residual 1.657 1.518 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C2' 6AD A 401 " pdb=" O2' 6AD A 401 " ideal model delta sigma weight residual 1.460 1.358 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C3' 6AD A 401 " pdb=" O3' 6AD A 401 " ideal model delta sigma weight residual 1.473 1.394 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 7145 not shown) Histogram of bond angle deviations from ideal: 96.43 - 104.08: 66 104.08 - 111.74: 3467 111.74 - 119.39: 2501 119.39 - 127.05: 3614 127.05 - 134.70: 68 Bond angle restraints: 9716 Sorted by residual: angle pdb=" N1 6AD A 401 " pdb=" C2 6AD A 401 " pdb=" S1 6AD A 401 " ideal model delta sigma weight residual 86.15 119.26 -33.11 3.00e+00 1.11e-01 1.22e+02 angle pdb=" N3 6AD A 401 " pdb=" C2 6AD A 401 " pdb=" S1 6AD A 401 " ideal model delta sigma weight residual 152.34 119.26 33.08 3.00e+00 1.11e-01 1.22e+02 angle pdb=" N1 6AD A 401 " pdb=" C6 6AD A 401 " pdb=" N6 6AD A 401 " ideal model delta sigma weight residual 104.75 121.30 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C5 6AD A 401 " pdb=" C6 6AD A 401 " pdb=" N6 6AD A 401 " ideal model delta sigma weight residual 134.98 120.50 14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N9 6AD A 401 " pdb=" C1' 6AD A 401 " pdb=" O4' 6AD A 401 " ideal model delta sigma weight residual 110.21 96.43 13.78 3.00e+00 1.11e-01 2.11e+01 ... (remaining 9711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 3868 17.42 - 34.85: 273 34.85 - 52.27: 49 52.27 - 69.69: 9 69.69 - 87.11: 8 Dihedral angle restraints: 4207 sinusoidal: 1556 harmonic: 2651 Sorted by residual: dihedral pdb=" CA SER C 331 " pdb=" C SER C 331 " pdb=" N TRP C 332 " pdb=" CA TRP C 332 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG C 19 " pdb=" CD ARG C 19 " pdb=" NE ARG C 19 " pdb=" CZ ARG C 19 " ideal model delta sinusoidal sigma weight residual -90.00 -134.69 44.69 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP C 298 " pdb=" CB ASP C 298 " pdb=" CG ASP C 298 " pdb=" OD1 ASP C 298 " ideal model delta sinusoidal sigma weight residual -30.00 -85.16 55.16 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 934 0.052 - 0.103: 178 0.103 - 0.155: 28 0.155 - 0.206: 0 0.206 - 0.258: 2 Chirality restraints: 1142 Sorted by residual: chirality pdb=" C3' 6AD A 401 " pdb=" C2' 6AD A 401 " pdb=" C4' 6AD A 401 " pdb=" O3' 6AD A 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.71 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C2' 6AD A 401 " pdb=" C1' 6AD A 401 " pdb=" C3' 6AD A 401 " pdb=" O2' 6AD A 401 " both_signs ideal model delta sigma weight residual False -2.44 -2.23 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE C 273 " pdb=" N ILE C 273 " pdb=" C ILE C 273 " pdb=" CB ILE C 273 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1139 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.057 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO G 60 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 134 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 135 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO A 295 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.040 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 553 2.74 - 3.28: 7291 3.28 - 3.82: 12177 3.82 - 4.36: 14183 4.36 - 4.90: 24437 Nonbonded interactions: 58641 Sorted by model distance: nonbonded pdb=" ND2 ASN C 119 " pdb=" O GLY C 144 " model vdw 2.202 2.520 nonbonded pdb=" O PHE A 300 " pdb=" NH2 ARG A 306 " model vdw 2.217 2.520 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.241 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP G 48 " model vdw 2.255 2.440 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.263 2.440 ... (remaining 58636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 3.950 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.307 7150 Z= 0.394 Angle : 0.776 33.111 9716 Z= 0.348 Chirality : 0.041 0.258 1142 Planarity : 0.005 0.083 1212 Dihedral : 12.850 87.115 2480 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.14 % Allowed : 0.27 % Favored : 99.59 % 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: 0.21 (0.29), residues: 895 helix: 2.02 (0.28), residues: 366 sheet: -0.11 (0.41), residues: 164 loop : -1.78 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 149 HIS 0.004 0.001 HIS C 62 PHE 0.017 0.001 PHE A 106 TYR 0.023 0.001 TYR A 105 ARG 0.005 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7697 (ttpp) cc_final: 0.7419 (tttt) REVERT: B 210 LYS cc_start: 0.7897 (pttm) cc_final: 0.7628 (ptpp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.9789 time to fit residues: 163.7405 Evaluate side-chains 114 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7150 Z= 0.202 Angle : 0.535 8.190 9716 Z= 0.271 Chirality : 0.040 0.137 1142 Planarity : 0.005 0.063 1212 Dihedral : 5.045 78.472 974 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.59 % Allowed : 12.93 % Favored : 84.49 % 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: 0.19 (0.29), residues: 895 helix: 1.90 (0.28), residues: 366 sheet: -0.28 (0.41), residues: 165 loop : -1.58 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 149 HIS 0.003 0.001 HIS C 62 PHE 0.024 0.002 PHE A 106 TYR 0.017 0.001 TYR A 109 ARG 0.008 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7557 (tttt) REVERT: B 208 GLU cc_start: 0.6814 (tp30) cc_final: 0.6543 (tp30) REVERT: C 228 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7048 (p0) outliers start: 19 outliers final: 6 residues processed: 128 average time/residue: 1.0282 time to fit residues: 139.8621 Evaluate side-chains 110 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.0370 chunk 24 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 187 HIS B 295 ASN C 91 HIS C 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7150 Z= 0.256 Angle : 0.556 9.686 9716 Z= 0.283 Chirality : 0.042 0.135 1142 Planarity : 0.005 0.058 1212 Dihedral : 5.278 75.971 974 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.81 % Allowed : 16.33 % Favored : 79.86 % 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: 0.02 (0.28), residues: 895 helix: 1.73 (0.27), residues: 369 sheet: -0.54 (0.41), residues: 155 loop : -1.54 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 149 HIS 0.004 0.001 HIS C 62 PHE 0.022 0.002 PHE B 192 TYR 0.010 0.001 TYR A 109 ARG 0.008 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7690 (tttt) REVERT: A 235 ASN cc_start: 0.7295 (t0) cc_final: 0.7068 (t160) REVERT: A 282 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7221 (p) REVERT: B 277 GLU cc_start: 0.6998 (pm20) cc_final: 0.6782 (pm20) REVERT: B 320 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7936 (mt) REVERT: C 75 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: C 228 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7088 (p0) REVERT: G 36 ASP cc_start: 0.7684 (m-30) cc_final: 0.7237 (m-30) outliers start: 28 outliers final: 9 residues processed: 135 average time/residue: 0.9517 time to fit residues: 137.2566 Evaluate side-chains 121 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7150 Z= 0.237 Angle : 0.557 8.510 9716 Z= 0.283 Chirality : 0.041 0.136 1142 Planarity : 0.004 0.055 1212 Dihedral : 5.396 74.600 974 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.27 % Allowed : 19.46 % Favored : 77.28 % 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: 0.01 (0.28), residues: 895 helix: 1.59 (0.27), residues: 375 sheet: -0.42 (0.40), residues: 153 loop : -1.50 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 214 PHE 0.013 0.002 PHE A 77 TYR 0.009 0.001 TYR C 264 ARG 0.007 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7740 (tttt) REVERT: A 179 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7141 (mtpp) REVERT: A 222 ARG cc_start: 0.7486 (mtm180) cc_final: 0.7247 (mtp180) REVERT: A 235 ASN cc_start: 0.7260 (t0) cc_final: 0.7042 (t160) REVERT: A 282 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7267 (p) REVERT: B 277 GLU cc_start: 0.6893 (pm20) cc_final: 0.6637 (pm20) REVERT: B 320 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7754 (mt) REVERT: C 228 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7201 (p0) REVERT: G 36 ASP cc_start: 0.7703 (m-30) cc_final: 0.7234 (m-30) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 0.9296 time to fit residues: 135.3356 Evaluate side-chains 122 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7150 Z= 0.217 Angle : 0.558 7.847 9716 Z= 0.287 Chirality : 0.040 0.129 1142 Planarity : 0.004 0.053 1212 Dihedral : 5.387 72.961 974 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.08 % Allowed : 19.46 % Favored : 76.46 % 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: 0.01 (0.28), residues: 895 helix: 1.58 (0.27), residues: 375 sheet: -0.43 (0.40), residues: 153 loop : -1.49 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.002 0.001 HIS A 253 PHE 0.014 0.001 PHE A 106 TYR 0.016 0.001 TYR A 109 ARG 0.010 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7743 (tttt) REVERT: A 179 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7059 (mtpp) REVERT: A 235 ASN cc_start: 0.7230 (t0) cc_final: 0.7027 (t160) REVERT: A 282 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7276 (p) REVERT: B 277 GLU cc_start: 0.6926 (pm20) cc_final: 0.6624 (pm20) REVERT: B 320 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 334 GLN cc_start: 0.8151 (tp40) cc_final: 0.7815 (tp40) REVERT: C 228 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7127 (p0) REVERT: G 36 ASP cc_start: 0.7751 (m-30) cc_final: 0.7275 (m-30) outliers start: 30 outliers final: 15 residues processed: 134 average time/residue: 0.8863 time to fit residues: 127.4318 Evaluate side-chains 123 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7150 Z= 0.237 Angle : 0.575 8.193 9716 Z= 0.295 Chirality : 0.041 0.129 1142 Planarity : 0.004 0.053 1212 Dihedral : 5.439 72.398 974 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.81 % Allowed : 20.95 % Favored : 75.24 % 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: 0.01 (0.28), residues: 895 helix: 1.66 (0.27), residues: 369 sheet: -0.36 (0.39), residues: 163 loop : -1.58 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 214 PHE 0.014 0.001 PHE A 106 TYR 0.010 0.001 TYR A 109 ARG 0.008 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7678 (tttt) REVERT: A 179 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7023 (mtpp) REVERT: A 282 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7397 (p) REVERT: B 277 GLU cc_start: 0.7030 (pm20) cc_final: 0.6733 (pm20) REVERT: B 320 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7666 (mt) REVERT: B 334 GLN cc_start: 0.8078 (tp40) cc_final: 0.7742 (tp40) REVERT: C 228 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7283 (p0) REVERT: C 262 MET cc_start: 0.7251 (pp-130) cc_final: 0.7041 (pp-130) REVERT: G 36 ASP cc_start: 0.7718 (m-30) cc_final: 0.7264 (m-30) outliers start: 28 outliers final: 16 residues processed: 128 average time/residue: 0.9289 time to fit residues: 127.2254 Evaluate side-chains 123 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7150 Z= 0.385 Angle : 0.660 9.884 9716 Z= 0.340 Chirality : 0.044 0.160 1142 Planarity : 0.005 0.054 1212 Dihedral : 5.784 74.317 974 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.27 % Allowed : 22.59 % Favored : 74.15 % 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: -0.30 (0.28), residues: 895 helix: 1.26 (0.27), residues: 373 sheet: -0.63 (0.37), residues: 178 loop : -1.59 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS B 214 PHE 0.016 0.002 PHE C 151 TYR 0.014 0.002 TYR A 109 ARG 0.007 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7853 (tttt) REVERT: A 179 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7086 (mtpp) REVERT: A 282 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7511 (p) REVERT: B 277 GLU cc_start: 0.7024 (pm20) cc_final: 0.6771 (pm20) REVERT: B 334 GLN cc_start: 0.8053 (tp40) cc_final: 0.7777 (tp40) REVERT: C 228 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7406 (p0) REVERT: G 36 ASP cc_start: 0.7931 (m-30) cc_final: 0.7576 (m-30) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 1.0146 time to fit residues: 143.3309 Evaluate side-chains 132 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 7150 Z= 0.253 Angle : 0.602 8.367 9716 Z= 0.310 Chirality : 0.041 0.161 1142 Planarity : 0.004 0.053 1212 Dihedral : 5.641 73.484 974 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.40 % Allowed : 23.40 % Favored : 73.20 % 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: -0.15 (0.28), residues: 895 helix: 1.50 (0.27), residues: 372 sheet: -0.75 (0.38), residues: 166 loop : -1.50 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.003 0.001 HIS A 253 PHE 0.014 0.001 PHE C 151 TYR 0.010 0.001 TYR A 109 ARG 0.007 0.001 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6931 (mtpp) REVERT: A 282 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 210 LYS cc_start: 0.7973 (pttm) cc_final: 0.7667 (ptpp) REVERT: B 277 GLU cc_start: 0.7032 (pm20) cc_final: 0.6783 (pm20) REVERT: B 320 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 228 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7391 (p0) REVERT: G 36 ASP cc_start: 0.7934 (m-30) cc_final: 0.7522 (m-30) outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 0.8806 time to fit residues: 128.4028 Evaluate side-chains 125 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 7150 Z= 0.281 Angle : 0.614 11.658 9716 Z= 0.315 Chirality : 0.041 0.157 1142 Planarity : 0.004 0.053 1212 Dihedral : 5.587 73.039 974 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.54 % Allowed : 24.90 % Favored : 71.56 % 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: -0.14 (0.28), residues: 895 helix: 1.50 (0.27), residues: 373 sheet: -0.80 (0.38), residues: 168 loop : -1.46 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.004 0.001 HIS C 311 PHE 0.015 0.001 PHE C 151 TYR 0.011 0.001 TYR A 109 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6991 (mtpp) REVERT: A 282 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7560 (p) REVERT: B 193 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8111 (mptt) REVERT: B 277 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: B 320 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7695 (mt) REVERT: B 334 GLN cc_start: 0.7995 (tp40) cc_final: 0.7784 (tp40) REVERT: C 101 MET cc_start: 0.8054 (ptm) cc_final: 0.7784 (mtm) REVERT: C 217 MET cc_start: 0.7265 (ppp) cc_final: 0.6799 (ppp) REVERT: C 228 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7425 (p0) REVERT: G 36 ASP cc_start: 0.7951 (m-30) cc_final: 0.7535 (m-30) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 0.8825 time to fit residues: 121.5508 Evaluate side-chains 128 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 7150 Z= 0.240 Angle : 0.592 10.189 9716 Z= 0.304 Chirality : 0.041 0.162 1142 Planarity : 0.004 0.053 1212 Dihedral : 5.518 71.901 974 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.86 % Allowed : 25.44 % Favored : 71.70 % 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: -0.11 (0.28), residues: 895 helix: 1.56 (0.27), residues: 373 sheet: -0.77 (0.38), residues: 166 loop : -1.49 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.003 0.001 HIS A 253 PHE 0.015 0.001 PHE C 151 TYR 0.012 0.001 TYR C 264 ARG 0.006 0.000 ARG C 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7540 (p) REVERT: B 274 LEU cc_start: 0.7575 (tt) cc_final: 0.7315 (tp) REVERT: B 277 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: B 320 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7691 (mt) REVERT: B 334 GLN cc_start: 0.7979 (tp40) cc_final: 0.7763 (tp40) REVERT: C 217 MET cc_start: 0.7241 (ppp) cc_final: 0.6796 (ppp) REVERT: C 228 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7289 (p0) REVERT: G 36 ASP cc_start: 0.7937 (m-30) cc_final: 0.7544 (m-30) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.8965 time to fit residues: 114.4306 Evaluate side-chains 119 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.0020 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.168398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125222 restraints weight = 7447.935| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3502 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 7150 Z= 0.233 Angle : 0.606 11.196 9716 Z= 0.307 Chirality : 0.040 0.158 1142 Planarity : 0.004 0.052 1212 Dihedral : 5.474 70.861 974 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.72 % Allowed : 25.58 % Favored : 71.70 % 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: -0.05 (0.28), residues: 895 helix: 1.62 (0.27), residues: 373 sheet: -0.62 (0.39), residues: 157 loop : -1.54 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS A 253 PHE 0.015 0.001 PHE C 151 TYR 0.011 0.001 TYR A 109 ARG 0.007 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.67 seconds wall clock time: 61 minutes 54.70 seconds (3714.70 seconds total)