Starting phenix.real_space_refine on Fri Nov 15 07:58:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j23_35943/11_2024/8j23_35943.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j23_35943/11_2024/8j23_35943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j23_35943/11_2024/8j23_35943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j23_35943/11_2024/8j23_35943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j23_35943/11_2024/8j23_35943.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j23_35943/11_2024/8j23_35943.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5494 2.51 5 N 1460 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8596 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2084 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 5.46, per 1000 atoms: 0.64 Number of scatterers: 8596 At special positions: 0 Unit cell: (117.52, 109.2, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1585 8.00 N 1460 7.00 C 5494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 994.3 milliseconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 37.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 4 through 38 removed outlier: 3.538A pdb=" N TYR A 14 " --> pdb=" O ILE A 10 " (cutoff:3.500A) Proline residue: A 23 - end of helix removed outlier: 3.527A pdb=" N GLY A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 61 removed outlier: 3.600A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.913A pdb=" N LYS A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 110 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.744A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 removed outlier: 3.791A pdb=" N GLY A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 144 " --> pdb=" O HIS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 204 Proline residue: A 177 - end of helix removed outlier: 3.746A pdb=" N ILE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix removed outlier: 3.726A pdb=" N ARG A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 247 removed outlier: 3.581A pdb=" N ARG A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.840A pdb=" N HIS A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 removed outlier: 3.663A pdb=" N VAL A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Proline residue: A 269 - end of helix removed outlier: 3.623A pdb=" N PHE A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.709A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.287A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.749A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.786A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.691A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.000A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 removed outlier: 9.231A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 49 removed outlier: 5.872A pdb=" N THR C 45 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C 338 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 47 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 334 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.544A pdb=" N ALA C 58 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 72 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP C 81 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS C 87 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 98 through 103 removed outlier: 7.029A pdb=" N GLY C 113 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS C 101 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 111 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR C 103 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR C 109 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS C 119 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU C 136 " --> pdb=" O CYS C 119 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 121 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 149 removed outlier: 3.719A pdb=" N THR C 176 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP C 168 " --> pdb=" O GLN C 174 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLN C 174 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.588A pdb=" N PHE C 197 " --> pdb=" O TRP C 209 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN C 218 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP C 210 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS C 216 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 232 removed outlier: 3.620A pdb=" N LEU C 250 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET C 260 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP C 252 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU C 258 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.833A pdb=" N SER C 273 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN C 291 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY C 304 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 296 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG C 302 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.585A pdb=" N THR F 115 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 94 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.585A pdb=" N THR F 115 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 94 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 98 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 132 through 135 Processing sheet with id=AB4, first strand: chain 'F' and resid 142 through 146 Processing sheet with id=AB5, first strand: chain 'F' and resid 180 through 181 removed outlier: 6.520A pdb=" N TRP F 162 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR F 176 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU F 160 " --> pdb=" O TYR F 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1182 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: 2.80 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2763 1.34 - 1.46: 2144 1.46 - 1.58: 3797 1.58 - 1.70: 0 1.70 - 1.81: 81 Bond restraints: 8785 Sorted by residual: bond pdb=" CB PRO A 123 " pdb=" CG PRO A 123 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.26e-02 6.30e+03 1.89e+00 bond pdb=" CG PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" CB PRO F 222 " pdb=" CG PRO F 222 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.66e+00 bond pdb=" CB ASN C 235 " pdb=" CG ASN C 235 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 8780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 11889 4.40 - 8.81: 18 8.81 - 13.21: 4 13.21 - 17.62: 0 17.62 - 22.02: 1 Bond angle restraints: 11912 Sorted by residual: angle pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 109.81 131.83 -22.02 2.21e+00 2.05e-01 9.93e+01 angle pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta sigma weight residual 119.84 132.25 -12.41 1.25e+00 6.40e-01 9.85e+01 angle pdb=" C PRO F 222 " pdb=" CA PRO F 222 " pdb=" CB PRO F 222 " ideal model delta sigma weight residual 111.56 124.71 -13.15 1.65e+00 3.67e-01 6.35e+01 angle pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" CD PRO F 222 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C GLU F 220 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " ideal model delta sigma weight residual 121.80 130.60 -8.80 2.44e+00 1.68e-01 1.30e+01 ... (remaining 11907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 4690 24.81 - 49.62: 453 49.62 - 74.43: 31 74.43 - 99.25: 7 99.25 - 124.06: 1 Dihedral angle restraints: 5182 sinusoidal: 1995 harmonic: 3187 Sorted by residual: dihedral pdb=" CA TYR F 221 " pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta harmonic sigma weight residual 180.00 55.94 124.06 0 5.00e+00 4.00e-02 6.16e+02 dihedral pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual 122.80 158.56 -35.76 0 2.50e+00 1.60e-01 2.05e+02 dihedral pdb=" C TYR F 221 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual -122.60 -158.33 35.73 0 2.50e+00 1.60e-01 2.04e+02 ... (remaining 5179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 1347 0.326 - 0.653: 0 0.653 - 0.979: 1 0.979 - 1.306: 0 1.306 - 1.632: 1 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA TYR F 221 " pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CB TYR F 221 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.66e+01 chirality pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" C PRO F 222 " pdb=" CB PRO F 222 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CA ILE F 100 " pdb=" N ILE F 100 " pdb=" C ILE F 100 " pdb=" CB ILE F 100 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1346 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 122 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO A 123 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 233 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO C 234 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 221 " -0.062 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO F 222 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " -0.042 5.00e-02 4.00e+02 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 150 2.67 - 3.23: 7875 3.23 - 3.79: 13577 3.79 - 4.34: 18090 4.34 - 4.90: 30431 Nonbonded interactions: 70123 Sorted by model distance: nonbonded pdb=" OG1 THR C 84 " pdb=" OD1 ASN C 86 " model vdw 2.116 3.040 nonbonded pdb=" O ILE C 56 " pdb=" OG SER C 314 " model vdw 2.183 3.040 nonbonded pdb=" OG SER C 106 " pdb=" OD1 ASN C 108 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 159 " pdb=" OD1 ASP C 161 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR C 63 " pdb=" O PRO C 105 " model vdw 2.265 3.040 ... (remaining 70118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.02 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.002 0.077 8785 Z= 0.151 Angle : 0.570 22.025 11912 Z= 0.295 Chirality : 0.062 1.632 1349 Planarity : 0.006 0.115 1504 Dihedral : 17.342 124.058 3125 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.49 % Rotamer: Outliers : 0.43 % Allowed : 30.60 % Favored : 68.97 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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: 0.73 (0.26), residues: 1083 helix: 1.42 (0.27), residues: 375 sheet: 0.86 (0.33), residues: 259 loop : -0.50 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 75 HIS 0.002 0.000 HIS F 35 PHE 0.028 0.001 PHE B 334 TYR 0.044 0.001 TYR F 221 ARG 0.004 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.8069 (m) cc_final: 0.7806 (p) REVERT: A 249 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5969 (tptm) REVERT: B 197 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7400 (mttp) REVERT: B 209 LYS cc_start: 0.7441 (ptmt) cc_final: 0.7174 (ptpp) REVERT: D 17 MET cc_start: 0.6721 (mmp) cc_final: 0.6513 (mmp) REVERT: F 39 GLN cc_start: 0.7687 (tt0) cc_final: 0.7451 (tt0) REVERT: F 126 MET cc_start: 0.7862 (tpp) cc_final: 0.7352 (tpp) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.2475 time to fit residues: 71.4350 Evaluate side-chains 205 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain B residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 264 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN F 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8785 Z= 0.287 Angle : 0.622 14.197 11912 Z= 0.325 Chirality : 0.045 0.318 1349 Planarity : 0.006 0.076 1504 Dihedral : 4.319 40.777 1195 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 5.71 % Allowed : 25.00 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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: 0.88 (0.26), residues: 1083 helix: 1.55 (0.27), residues: 391 sheet: 0.82 (0.33), residues: 258 loop : -0.40 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 75 HIS 0.005 0.001 HIS C 89 PHE 0.021 0.002 PHE B 259 TYR 0.019 0.002 TYR F 59 ARG 0.008 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 1.003 Fit side-chains REVERT: A 119 LEU cc_start: 0.7032 (pt) cc_final: 0.6596 (pp) REVERT: A 184 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6368 (tt) REVERT: A 186 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6895 (tp) REVERT: A 267 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7297 (tt) REVERT: A 270 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7367 (tt) REVERT: A 273 TYR cc_start: 0.4704 (OUTLIER) cc_final: 0.4068 (p90) REVERT: B 46 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6501 (mttp) REVERT: B 197 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7479 (mtpp) REVERT: B 209 LYS cc_start: 0.7634 (ptmt) cc_final: 0.7427 (ptmt) REVERT: B 259 PHE cc_start: 0.8104 (m-10) cc_final: 0.7758 (m-80) REVERT: B 312 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7571 (mttp) REVERT: C 23 CYS cc_start: 0.8089 (m) cc_final: 0.7718 (m) REVERT: C 47 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7026 (mpt180) REVERT: C 66 ARG cc_start: 0.6836 (ttp-170) cc_final: 0.5937 (ttp80) REVERT: C 203 ASP cc_start: 0.7250 (p0) cc_final: 0.7043 (p0) REVERT: F 39 GLN cc_start: 0.7995 (tt0) cc_final: 0.7760 (tt0) outliers start: 53 outliers final: 23 residues processed: 245 average time/residue: 0.2312 time to fit residues: 75.9864 Evaluate side-chains 245 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 0.0010 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN B 213 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8785 Z= 0.244 Angle : 0.577 11.746 11912 Z= 0.294 Chirality : 0.044 0.324 1349 Planarity : 0.005 0.069 1504 Dihedral : 4.234 31.098 1191 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 5.17 % Allowed : 24.78 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.86 (0.26), residues: 1083 helix: 1.62 (0.27), residues: 396 sheet: 0.63 (0.32), residues: 268 loop : -0.42 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 75 HIS 0.004 0.001 HIS B 195 PHE 0.016 0.002 PHE C 197 TYR 0.016 0.002 TYR F 59 ARG 0.006 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6400 (tt) REVERT: A 270 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 273 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.4161 (p90) REVERT: B 209 LYS cc_start: 0.7721 (ptmt) cc_final: 0.7503 (ptmt) REVERT: B 312 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7692 (mttp) REVERT: C 23 CYS cc_start: 0.8085 (m) cc_final: 0.7731 (m) REVERT: C 47 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7228 (mpt180) REVERT: C 168 ASP cc_start: 0.7157 (t0) cc_final: 0.6922 (t0) REVERT: C 203 ASP cc_start: 0.7444 (p0) cc_final: 0.7241 (p0) REVERT: C 264 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8475 (t-90) outliers start: 48 outliers final: 27 residues processed: 233 average time/residue: 0.2258 time to fit residues: 70.7277 Evaluate side-chains 242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 HIS F 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8785 Z= 0.283 Angle : 0.590 9.867 11912 Z= 0.300 Chirality : 0.045 0.319 1349 Planarity : 0.006 0.103 1504 Dihedral : 4.326 28.859 1190 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 5.93 % Allowed : 23.92 % Favored : 70.15 % 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: 0.75 (0.26), residues: 1083 helix: 1.63 (0.27), residues: 397 sheet: 0.48 (0.31), residues: 272 loop : -0.54 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 75 HIS 0.005 0.001 HIS B 195 PHE 0.019 0.002 PHE C 197 TYR 0.016 0.002 TYR F 59 ARG 0.007 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.7069 (tpp) cc_final: 0.6632 (ttp) REVERT: A 184 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6448 (tt) REVERT: A 273 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4255 (p90) REVERT: B 46 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6573 (mttm) REVERT: B 200 ASP cc_start: 0.7743 (t0) cc_final: 0.7541 (t0) REVERT: B 209 LYS cc_start: 0.7824 (ptmt) cc_final: 0.7594 (ptmt) REVERT: B 312 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7657 (mttp) REVERT: C 23 CYS cc_start: 0.8097 (m) cc_final: 0.7742 (m) REVERT: C 47 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7143 (mpt180) REVERT: C 211 VAL cc_start: 0.8126 (t) cc_final: 0.7911 (m) REVERT: C 217 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7637 (mtt90) REVERT: C 226 ASP cc_start: 0.7860 (p0) cc_final: 0.7499 (p0) REVERT: F 200 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7879 (tp) REVERT: F 216 MET cc_start: 0.7877 (ttp) cc_final: 0.7641 (ttp) outliers start: 55 outliers final: 35 residues processed: 251 average time/residue: 0.2444 time to fit residues: 82.0108 Evaluate side-chains 252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8785 Z= 0.286 Angle : 0.591 11.689 11912 Z= 0.301 Chirality : 0.045 0.292 1349 Planarity : 0.005 0.102 1504 Dihedral : 4.393 24.864 1190 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 6.79 % Allowed : 22.74 % Favored : 70.47 % 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: 0.62 (0.26), residues: 1083 helix: 1.57 (0.27), residues: 402 sheet: 0.35 (0.31), residues: 268 loop : -0.65 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 75 HIS 0.004 0.001 HIS B 195 PHE 0.020 0.002 PHE C 197 TYR 0.014 0.002 TYR F 59 ARG 0.005 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6423 (tt) REVERT: A 273 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.4303 (p90) REVERT: B 46 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6637 (mttm) REVERT: B 209 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7576 (ptmt) REVERT: B 243 MET cc_start: 0.8257 (tpp) cc_final: 0.8040 (tpp) REVERT: B 312 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7639 (mttm) REVERT: C 23 CYS cc_start: 0.8141 (m) cc_final: 0.7774 (m) REVERT: C 47 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7084 (mpt180) REVERT: C 59 MET cc_start: 0.8238 (tmm) cc_final: 0.7976 (tmm) REVERT: C 186 MET cc_start: 0.8483 (mtp) cc_final: 0.8186 (mtp) REVERT: C 211 VAL cc_start: 0.8243 (t) cc_final: 0.8011 (m) REVERT: C 226 ASP cc_start: 0.7883 (p0) cc_final: 0.7465 (p0) REVERT: C 264 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8491 (t-90) REVERT: F 200 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7915 (tp) outliers start: 63 outliers final: 46 residues processed: 256 average time/residue: 0.2375 time to fit residues: 80.7273 Evaluate side-chains 268 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 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 140 HIS B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8785 Z= 0.233 Angle : 0.569 12.567 11912 Z= 0.290 Chirality : 0.043 0.270 1349 Planarity : 0.005 0.101 1504 Dihedral : 4.324 25.508 1190 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 5.60 % Allowed : 24.35 % Favored : 70.04 % 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: 0.66 (0.26), residues: 1083 helix: 1.69 (0.27), residues: 402 sheet: 0.23 (0.31), residues: 272 loop : -0.61 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 75 HIS 0.003 0.001 HIS C 140 PHE 0.019 0.002 PHE C 197 TYR 0.015 0.001 TYR F 101 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.970 Fit side-chains REVERT: A 12 MET cc_start: 0.5790 (mmm) cc_final: 0.5573 (mmm) REVERT: A 180 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4820 (tt) REVERT: A 184 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6380 (tt) REVERT: A 273 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4273 (p90) REVERT: B 46 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6572 (mttm) REVERT: B 186 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 197 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7649 (mtpp) REVERT: B 209 LYS cc_start: 0.7794 (ptmt) cc_final: 0.7568 (ptmt) REVERT: B 312 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7612 (mttm) REVERT: C 23 CYS cc_start: 0.8152 (m) cc_final: 0.7786 (m) REVERT: C 47 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7022 (mpt180) REVERT: C 59 MET cc_start: 0.8220 (tmm) cc_final: 0.7962 (tmm) REVERT: C 186 MET cc_start: 0.8496 (mtp) cc_final: 0.8185 (mtp) REVERT: C 217 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7688 (mtt-85) REVERT: C 226 ASP cc_start: 0.7851 (p0) cc_final: 0.7431 (p0) REVERT: C 302 ARG cc_start: 0.7512 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: F 200 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7910 (tp) REVERT: F 216 MET cc_start: 0.7778 (ttp) cc_final: 0.7491 (ttp) outliers start: 52 outliers final: 38 residues processed: 241 average time/residue: 0.2543 time to fit residues: 81.2593 Evaluate side-chains 258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8785 Z= 0.296 Angle : 0.593 13.243 11912 Z= 0.303 Chirality : 0.044 0.271 1349 Planarity : 0.005 0.096 1504 Dihedral : 4.425 25.160 1190 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 6.36 % Allowed : 24.57 % Favored : 69.07 % 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: 0.52 (0.26), residues: 1083 helix: 1.55 (0.27), residues: 405 sheet: 0.16 (0.31), residues: 264 loop : -0.67 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 80 HIS 0.005 0.001 HIS C 140 PHE 0.021 0.002 PHE C 197 TYR 0.016 0.002 TYR F 101 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6412 (tt) REVERT: A 273 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.4336 (p90) REVERT: B 46 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6727 (mttm) REVERT: B 186 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 197 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7618 (mtpp) REVERT: B 209 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7593 (ptmt) REVERT: B 312 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7618 (mttm) REVERT: C 23 CYS cc_start: 0.8161 (m) cc_final: 0.7800 (m) REVERT: C 47 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7023 (mpt180) REVERT: C 59 MET cc_start: 0.8223 (tmm) cc_final: 0.7955 (tmm) REVERT: C 186 MET cc_start: 0.8481 (mtp) cc_final: 0.8180 (mtp) REVERT: C 211 VAL cc_start: 0.8195 (t) cc_final: 0.7953 (m) REVERT: C 217 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7718 (mtt-85) REVERT: C 226 ASP cc_start: 0.7855 (p0) cc_final: 0.7391 (p0) REVERT: C 298 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (mt) REVERT: C 302 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7203 (mmm-85) REVERT: F 200 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7929 (tp) REVERT: F 223 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7896 (mp) outliers start: 59 outliers final: 43 residues processed: 247 average time/residue: 0.2371 time to fit residues: 77.9536 Evaluate side-chains 261 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8785 Z= 0.266 Angle : 0.596 13.407 11912 Z= 0.301 Chirality : 0.044 0.265 1349 Planarity : 0.005 0.096 1504 Dihedral : 4.431 25.809 1190 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 5.82 % Allowed : 25.22 % Favored : 68.97 % 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: 0.51 (0.26), residues: 1083 helix: 1.59 (0.27), residues: 404 sheet: 0.05 (0.31), residues: 266 loop : -0.65 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 80 HIS 0.005 0.001 HIS C 140 PHE 0.019 0.002 PHE C 197 TYR 0.017 0.001 TYR F 101 ARG 0.007 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.5832 (mmm) cc_final: 0.5590 (mmm) REVERT: A 273 TYR cc_start: 0.5220 (OUTLIER) cc_final: 0.4412 (p90) REVERT: B 46 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6665 (mttm) REVERT: B 197 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7618 (mtpp) REVERT: B 209 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7574 (ptmt) REVERT: B 312 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7625 (mttm) REVERT: C 23 CYS cc_start: 0.8172 (m) cc_final: 0.7815 (m) REVERT: C 47 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6932 (mpt180) REVERT: C 59 MET cc_start: 0.8233 (tmm) cc_final: 0.7962 (tmm) REVERT: C 186 MET cc_start: 0.8501 (mtp) cc_final: 0.8196 (mtp) REVERT: C 217 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7736 (mtt-85) REVERT: C 226 ASP cc_start: 0.7836 (p0) cc_final: 0.7366 (p0) REVERT: C 302 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7205 (mmm-85) REVERT: F 200 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7946 (tp) REVERT: F 213 TYR cc_start: 0.7891 (m-80) cc_final: 0.7600 (m-10) REVERT: F 216 MET cc_start: 0.7760 (ttp) cc_final: 0.7496 (ttp) REVERT: F 223 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7833 (mp) outliers start: 54 outliers final: 44 residues processed: 239 average time/residue: 0.2531 time to fit residues: 79.6950 Evaluate side-chains 260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 chunk 29 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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: 0.7244 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8785 Z= 0.164 Angle : 0.555 12.897 11912 Z= 0.280 Chirality : 0.042 0.238 1349 Planarity : 0.005 0.094 1504 Dihedral : 4.215 26.510 1190 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 4.96 % Allowed : 26.08 % Favored : 68.97 % 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: 0.70 (0.26), residues: 1083 helix: 1.76 (0.27), residues: 402 sheet: 0.25 (0.31), residues: 268 loop : -0.62 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 80 HIS 0.004 0.001 HIS F 35 PHE 0.015 0.001 PHE C 197 TYR 0.010 0.001 TYR F 176 ARG 0.006 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.5673 (mmm) cc_final: 0.5395 (mmm) REVERT: A 105 ILE cc_start: 0.8203 (mt) cc_final: 0.7963 (tt) REVERT: A 273 TYR cc_start: 0.5174 (OUTLIER) cc_final: 0.4401 (p90) REVERT: B 46 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6458 (mttm) REVERT: B 197 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7659 (mtpp) REVERT: B 209 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7544 (ptmt) REVERT: B 312 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7618 (mttm) REVERT: C 23 CYS cc_start: 0.8128 (m) cc_final: 0.7705 (m) REVERT: C 47 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6959 (mpt180) REVERT: C 59 MET cc_start: 0.8229 (tmm) cc_final: 0.7974 (tmm) REVERT: C 186 MET cc_start: 0.8496 (mtp) cc_final: 0.8203 (mtp) REVERT: C 211 VAL cc_start: 0.8152 (t) cc_final: 0.7880 (m) REVERT: C 217 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7709 (mtt-85) REVERT: C 226 ASP cc_start: 0.7765 (p0) cc_final: 0.7337 (p0) REVERT: F 200 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7908 (tp) REVERT: F 216 MET cc_start: 0.7723 (ttp) cc_final: 0.7495 (ttp) REVERT: F 223 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7829 (mp) outliers start: 46 outliers final: 34 residues processed: 236 average time/residue: 0.2586 time to fit residues: 79.4465 Evaluate side-chains 248 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8785 Z= 0.226 Angle : 0.575 8.919 11912 Z= 0.289 Chirality : 0.043 0.218 1349 Planarity : 0.005 0.084 1504 Dihedral : 4.269 26.148 1190 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.63 % Allowed : 26.62 % Favored : 68.75 % 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: 0.64 (0.26), residues: 1083 helix: 1.69 (0.27), residues: 405 sheet: 0.18 (0.31), residues: 272 loop : -0.63 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 80 HIS 0.004 0.001 HIS C 140 PHE 0.018 0.002 PHE C 197 TYR 0.016 0.001 TYR F 221 ARG 0.007 0.000 ARG F 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.5719 (mmm) cc_final: 0.5410 (mmm) REVERT: A 105 ILE cc_start: 0.8222 (mt) cc_final: 0.7976 (tt) REVERT: A 273 TYR cc_start: 0.5025 (OUTLIER) cc_final: 0.4328 (p90) REVERT: B 46 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6543 (mttm) REVERT: B 197 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7684 (mtpp) REVERT: B 209 LYS cc_start: 0.7793 (ptmt) cc_final: 0.7558 (ptmt) REVERT: B 312 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7635 (mttm) REVERT: C 23 CYS cc_start: 0.8156 (m) cc_final: 0.7736 (m) REVERT: C 47 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6955 (mpt180) REVERT: C 59 MET cc_start: 0.8255 (tmm) cc_final: 0.8002 (tmm) REVERT: C 186 MET cc_start: 0.8482 (mtp) cc_final: 0.8206 (mtp) REVERT: C 195 ARG cc_start: 0.7224 (mmt-90) cc_final: 0.6901 (mmm-85) REVERT: C 211 VAL cc_start: 0.8211 (t) cc_final: 0.7951 (m) REVERT: C 217 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7756 (mtt-85) REVERT: C 226 ASP cc_start: 0.7819 (p0) cc_final: 0.7368 (p0) REVERT: C 281 ARG cc_start: 0.8259 (tpt170) cc_final: 0.8040 (tpt170) REVERT: F 200 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7921 (tp) REVERT: F 216 MET cc_start: 0.7743 (ttp) cc_final: 0.7465 (ttp) REVERT: F 223 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7820 (mp) outliers start: 43 outliers final: 34 residues processed: 235 average time/residue: 0.2508 time to fit residues: 77.1911 Evaluate side-chains 252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.0000 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129727 restraints weight = 11821.132| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.10 r_work: 0.3457 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8785 Z= 0.235 Angle : 0.581 8.449 11912 Z= 0.292 Chirality : 0.043 0.202 1349 Planarity : 0.005 0.091 1504 Dihedral : 4.330 26.203 1190 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.85 % Allowed : 26.83 % Favored : 68.32 % 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: 0.59 (0.26), residues: 1083 helix: 1.65 (0.27), residues: 405 sheet: 0.11 (0.31), residues: 274 loop : -0.62 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 80 HIS 0.005 0.001 HIS C 140 PHE 0.018 0.002 PHE C 197 TYR 0.017 0.001 TYR F 101 ARG 0.008 0.000 ARG F 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.35 seconds wall clock time: 47 minutes 20.34 seconds (2840.34 seconds total)