Starting phenix.real_space_refine on Tue Jan 14 11:32:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1c_61971/01_2025/9k1c_61971.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1c_61971/01_2025/9k1c_61971.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/cci-nas-00/data/ceres_data/9k1c_61971/01_2025/9k1c_61971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1c_61971/01_2025/9k1c_61971.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1c_61971/01_2025/9k1c_61971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1c_61971/01_2025/9k1c_61971.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= 0.004 sd= 0.117 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 46 5.16 5 C 4220 2.51 5 N 1140 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6611 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1982 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 20, 'TRANS': 258} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.27, per 1000 atoms: 0.65 Number of scatterers: 6611 At special positions: 0 Unit cell: (77.112, 98.532, 131.733, 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 46 16.00 O 1205 8.00 N 1140 7.00 C 4220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " 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: 1.60 Conformation dependent library (CDL) restraints added in 919.8 milliseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 44.3% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 3.528A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 66 removed outlier: 3.537A pdb=" N TYR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 110 Proline residue: R 89 - end of helix removed outlier: 3.803A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 117 Processing helix chain 'R' and resid 119 through 146 removed outlier: 3.682A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 removed outlier: 5.139A pdb=" N LEU R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Proline residue: R 194 - end of helix Processing helix chain 'R' and resid 215 through 250 Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 256 through 276 removed outlier: 3.551A pdb=" N SER R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.100A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.849A pdb=" N GLY A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 4.408A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.176A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.179A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.644A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.933A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.634A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.109A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.731A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.629A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.675A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.660A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 336 hydrogen bonds defined for protein. 984 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: 1.94 Time building geometry restraints manager: 1.80 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: 2155 1.35 - 1.46: 1621 1.46 - 1.58: 2918 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6754 Sorted by residual: bond pdb=" C20 HXA R 401 " pdb=" C21 HXA R 401 " ideal model delta sigma weight residual 1.497 1.566 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C17 HXA R 401 " pdb=" C18 HXA R 401 " ideal model delta sigma weight residual 1.501 1.559 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C18 HXA R 401 " pdb=" C19 HXA R 401 " ideal model delta sigma weight residual 1.503 1.559 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" C15 HXA R 401 " pdb=" C16 HXA R 401 " ideal model delta sigma weight residual 1.502 1.546 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C3 HXA R 401 " pdb=" C4 HXA R 401 " ideal model delta sigma weight residual 1.496 1.534 -0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 6749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.90: 9154 5.90 - 11.80: 3 11.80 - 17.70: 5 17.70 - 23.60: 0 23.60 - 29.49: 7 Bond angle restraints: 9169 Sorted by residual: angle pdb=" C18 HXA R 401 " pdb=" C19 HXA R 401 " pdb=" C20 HXA R 401 " ideal model delta sigma weight residual 127.19 97.70 29.49 3.00e+00 1.11e-01 9.67e+01 angle pdb=" C12 HXA R 401 " pdb=" C13 HXA R 401 " pdb=" C14 HXA R 401 " ideal model delta sigma weight residual 127.67 153.55 -25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" C11 HXA R 401 " pdb=" C12 HXA R 401 " pdb=" C13 HXA R 401 " ideal model delta sigma weight residual 110.71 136.06 -25.35 3.00e+00 1.11e-01 7.14e+01 angle pdb=" C6 HXA R 401 " pdb=" C7 HXA R 401 " pdb=" C8 HXA R 401 " ideal model delta sigma weight residual 127.48 152.77 -25.29 3.00e+00 1.11e-01 7.11e+01 angle pdb=" C11 HXA R 401 " pdb=" C10 HXA R 401 " pdb=" C9 HXA R 401 " ideal model delta sigma weight residual 127.25 152.14 -24.89 3.00e+00 1.11e-01 6.89e+01 ... (remaining 9164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3568 17.01 - 34.02: 329 34.02 - 51.03: 69 51.03 - 68.04: 7 68.04 - 85.05: 7 Dihedral angle restraints: 3980 sinusoidal: 1476 harmonic: 2504 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 178.05 -85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS R 79 " pdb=" SG CYS R 79 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 153.08 -60.08 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB GLU A 308 " pdb=" CG GLU A 308 " pdb=" CD GLU A 308 " pdb=" OE1 GLU A 308 " ideal model delta sinusoidal sigma weight residual 0.00 -83.37 83.37 1 3.00e+01 1.11e-03 9.43e+00 ... (remaining 3977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 677 0.025 - 0.051: 221 0.051 - 0.076: 75 0.076 - 0.102: 47 0.102 - 0.127: 26 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ASP A 309 " pdb=" N ASP A 309 " pdb=" C ASP A 309 " pdb=" CB ASP A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 1043 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 238 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO R 239 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C THR B 87 " 0.024 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 236 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 730 2.75 - 3.29: 6215 3.29 - 3.83: 11069 3.83 - 4.36: 12172 4.36 - 4.90: 22132 Nonbonded interactions: 52318 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.262 3.040 nonbonded pdb=" O ASP R 175 " pdb=" OG SER R 178 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.285 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.308 3.040 ... (remaining 52313 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=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: 0.790 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.069 6754 Z= 0.159 Angle : 0.917 29.494 9169 Z= 0.357 Chirality : 0.036 0.127 1046 Planarity : 0.003 0.036 1173 Dihedral : 13.741 83.366 2360 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.31), residues: 859 helix: 3.30 (0.28), residues: 368 sheet: 1.33 (0.45), residues: 150 loop : -0.33 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 131 HIS 0.001 0.000 HIS B 183 PHE 0.007 0.001 PHE R 184 TYR 0.008 0.000 TYR B 111 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.688 Fit side-chains REVERT: A 231 ASP cc_start: 0.8213 (t70) cc_final: 0.7948 (t0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2028 time to fit residues: 25.7409 Evaluate side-chains 77 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.183142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138269 restraints weight = 6833.409| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.82 r_work: 0.3335 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.187 Angle : 0.510 8.430 9169 Z= 0.252 Chirality : 0.039 0.146 1046 Planarity : 0.003 0.033 1173 Dihedral : 5.463 58.133 948 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.89 % Allowed : 8.57 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.30), residues: 859 helix: 3.13 (0.28), residues: 371 sheet: 0.82 (0.41), residues: 162 loop : -0.33 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.011 0.001 PHE R 82 TYR 0.010 0.001 TYR R 250 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.720 Fit side-chains REVERT: B 156 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8239 (mt0) REVERT: B 215 GLU cc_start: 0.7483 (pt0) cc_final: 0.7054 (pt0) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.1994 time to fit residues: 19.9309 Evaluate side-chains 71 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.178252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133580 restraints weight = 6831.625| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.94 r_work: 0.3361 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6754 Z= 0.208 Angle : 0.504 8.891 9169 Z= 0.250 Chirality : 0.039 0.134 1046 Planarity : 0.003 0.033 1173 Dihedral : 5.398 53.263 948 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.33 % Allowed : 12.26 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.30), residues: 859 helix: 3.11 (0.28), residues: 369 sheet: 0.67 (0.41), residues: 160 loop : -0.53 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 131 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE R 82 TYR 0.008 0.001 TYR R 202 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.750 Fit side-chains REVERT: B 156 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8265 (mt0) REVERT: B 215 GLU cc_start: 0.7503 (pt0) cc_final: 0.7062 (pt0) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.2392 time to fit residues: 26.6021 Evaluate side-chains 87 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131413 restraints weight = 6859.957| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.93 r_work: 0.3205 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6754 Z= 0.232 Angle : 0.510 9.130 9169 Z= 0.252 Chirality : 0.039 0.131 1046 Planarity : 0.003 0.035 1173 Dihedral : 5.501 55.008 948 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.07 % Allowed : 13.00 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 859 helix: 3.03 (0.28), residues: 369 sheet: 0.49 (0.42), residues: 166 loop : -0.62 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.002 0.001 HIS B 266 PHE 0.013 0.001 PHE A 189 TYR 0.010 0.001 TYR R 202 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: B 212 ASP cc_start: 0.7828 (m-30) cc_final: 0.7622 (m-30) REVERT: B 215 GLU cc_start: 0.7594 (pt0) cc_final: 0.7101 (pt0) REVERT: B 269 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6605 (pt) REVERT: B 327 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8143 (p) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.1923 time to fit residues: 24.9211 Evaluate side-chains 94 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.175458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131250 restraints weight = 6888.961| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.88 r_work: 0.3205 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6754 Z= 0.202 Angle : 0.498 8.335 9169 Z= 0.247 Chirality : 0.039 0.132 1046 Planarity : 0.003 0.035 1173 Dihedral : 5.446 53.960 948 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.22 % Allowed : 14.33 % Favored : 83.46 % 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: 1.79 (0.30), residues: 859 helix: 3.01 (0.28), residues: 369 sheet: 0.53 (0.43), residues: 166 loop : -0.67 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR R 202 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: B 212 ASP cc_start: 0.7922 (m-30) cc_final: 0.7694 (m-30) REVERT: B 215 GLU cc_start: 0.7655 (pt0) cc_final: 0.7263 (pt0) REVERT: B 234 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8971 (m-80) REVERT: B 269 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6562 (pt) REVERT: B 327 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8174 (p) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.1949 time to fit residues: 24.7449 Evaluate side-chains 94 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131718 restraints weight = 6770.377| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.86 r_work: 0.3206 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6754 Z= 0.182 Angle : 0.497 8.028 9169 Z= 0.245 Chirality : 0.038 0.131 1046 Planarity : 0.003 0.036 1173 Dihedral : 5.389 53.408 948 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.36 % Allowed : 15.51 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.31), residues: 859 helix: 3.02 (0.28), residues: 369 sheet: 0.55 (0.43), residues: 166 loop : -0.71 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.002 0.001 HIS B 266 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR R 202 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.646 Fit side-chains REVERT: R 140 LEU cc_start: 0.7237 (tt) cc_final: 0.6813 (mt) REVERT: B 125 ASN cc_start: 0.8588 (t0) cc_final: 0.8357 (t0) REVERT: B 215 GLU cc_start: 0.7838 (pt0) cc_final: 0.7560 (pt0) REVERT: B 219 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7677 (mtt90) REVERT: B 234 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8971 (m-80) REVERT: B 269 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6508 (pt) REVERT: B 304 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7515 (mtm180) REVERT: B 327 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8191 (p) outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 0.2110 time to fit residues: 26.7080 Evaluate side-chains 97 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.172467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128843 restraints weight = 6849.589| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.85 r_work: 0.3170 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6754 Z= 0.246 Angle : 0.531 8.370 9169 Z= 0.264 Chirality : 0.040 0.130 1046 Planarity : 0.003 0.036 1173 Dihedral : 5.550 52.173 948 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.36 % Allowed : 15.66 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 859 helix: 2.84 (0.28), residues: 373 sheet: 0.45 (0.44), residues: 159 loop : -0.80 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.014 0.001 PHE A 189 TYR 0.008 0.001 TYR R 202 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.708 Fit side-chains REVERT: R 140 LEU cc_start: 0.7252 (tt) cc_final: 0.6808 (mt) REVERT: B 215 GLU cc_start: 0.7970 (pt0) cc_final: 0.7550 (pt0) REVERT: B 217 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: B 234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8989 (m-80) REVERT: B 269 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6574 (pt) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.1918 time to fit residues: 25.0191 Evaluate side-chains 99 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 156 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.173727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128595 restraints weight = 6876.261| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.93 r_work: 0.3166 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6754 Z= 0.208 Angle : 0.522 8.023 9169 Z= 0.257 Chirality : 0.039 0.134 1046 Planarity : 0.003 0.037 1173 Dihedral : 5.531 53.421 948 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.22 % Allowed : 15.81 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.30), residues: 859 helix: 2.90 (0.28), residues: 369 sheet: 0.47 (0.44), residues: 159 loop : -0.87 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 131 HIS 0.002 0.001 HIS B 311 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR R 202 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.760 Fit side-chains REVERT: R 140 LEU cc_start: 0.7206 (tt) cc_final: 0.6783 (mt) REVERT: B 125 ASN cc_start: 0.8603 (t0) cc_final: 0.8357 (t0) REVERT: B 215 GLU cc_start: 0.7937 (pt0) cc_final: 0.7530 (pt0) REVERT: B 217 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7347 (pmm) REVERT: B 226 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8265 (mt-10) REVERT: B 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: B 269 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6513 (pt) REVERT: B 327 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8286 (p) outliers start: 15 outliers final: 10 residues processed: 99 average time/residue: 0.2156 time to fit residues: 27.8479 Evaluate side-chains 100 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.173864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129109 restraints weight = 6884.697| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.92 r_work: 0.3179 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6754 Z= 0.192 Angle : 0.529 10.782 9169 Z= 0.258 Chirality : 0.039 0.135 1046 Planarity : 0.003 0.037 1173 Dihedral : 5.547 54.396 948 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.22 % Allowed : 15.51 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 859 helix: 2.92 (0.28), residues: 369 sheet: 0.46 (0.44), residues: 159 loop : -0.87 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.002 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 202 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.668 Fit side-chains REVERT: R 140 LEU cc_start: 0.7246 (tt) cc_final: 0.6817 (mt) REVERT: B 125 ASN cc_start: 0.8548 (t0) cc_final: 0.8346 (t0) REVERT: B 215 GLU cc_start: 0.7967 (pt0) cc_final: 0.7556 (pt0) REVERT: B 217 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7226 (pmm) REVERT: B 226 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 234 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8965 (m-80) REVERT: B 269 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6534 (pt) REVERT: B 327 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8288 (p) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.2117 time to fit residues: 27.3423 Evaluate side-chains 101 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.174774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130539 restraints weight = 6914.081| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.89 r_work: 0.3194 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6754 Z= 0.163 Angle : 0.519 9.695 9169 Z= 0.254 Chirality : 0.038 0.130 1046 Planarity : 0.003 0.038 1173 Dihedral : 5.523 58.997 948 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.22 % Allowed : 15.81 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 859 helix: 3.01 (0.28), residues: 368 sheet: 0.35 (0.44), residues: 165 loop : -0.80 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 131 HIS 0.002 0.000 HIS A 188 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 202 ARG 0.006 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.686 Fit side-chains REVERT: R 140 LEU cc_start: 0.7209 (tt) cc_final: 0.6787 (mt) REVERT: B 125 ASN cc_start: 0.8473 (t0) cc_final: 0.8258 (t0) REVERT: B 215 GLU cc_start: 0.8001 (pt0) cc_final: 0.7679 (pt0) REVERT: B 217 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7317 (pmm) REVERT: B 226 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 234 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: B 269 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6458 (pt) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.2169 time to fit residues: 29.4706 Evaluate side-chains 105 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.171805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127215 restraints weight = 6921.793| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.05 r_work: 0.3132 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6754 Z= 0.264 Angle : 0.567 10.682 9169 Z= 0.279 Chirality : 0.040 0.131 1046 Planarity : 0.004 0.038 1173 Dihedral : 5.562 56.385 948 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.36 % Allowed : 15.66 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.30), residues: 859 helix: 2.88 (0.28), residues: 368 sheet: 0.48 (0.45), residues: 157 loop : -0.88 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.008 0.001 TYR R 202 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.52 seconds wall clock time: 72 minutes 37.80 seconds (4357.80 seconds total)