Starting phenix.real_space_refine on Tue Sep 24 09:16:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zcj_39931/09_2024/8zcj_39931.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zcj_39931/09_2024/8zcj_39931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zcj_39931/09_2024/8zcj_39931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zcj_39931/09_2024/8zcj_39931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zcj_39931/09_2024/8zcj_39931.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zcj_39931/09_2024/8zcj_39931.cif" } resolution = 3.09 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= 0.007 sd= 0.096 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 41 5.16 5 C 4945 2.51 5 N 1344 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7808 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1556 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2369 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 131 Chain: "D" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 296 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1705 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "G" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1818 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 14, 'TRANS': 260} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 2, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 186 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'004:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.05, per 1000 atoms: 0.77 Number of scatterers: 7808 At special positions: 0 Unit cell: (85.6, 121.98, 121.98, 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 41 16.00 O 1478 8.00 N 1344 7.00 C 4945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 114 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS G 112 " - pdb=" SG CYS G 186 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR A 2 " Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 32.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.610A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.614A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.708A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.664A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 329 through 349 removed outlier: 4.233A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 34 through 44 removed outlier: 4.414A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing helix chain 'G' and resid 44 through 66 Processing helix chain 'G' and resid 73 through 92 removed outlier: 3.973A pdb=" N GLY G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 removed outlier: 4.161A pdb=" N THR G 98 " --> pdb=" O PRO G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 142 removed outlier: 4.319A pdb=" N GLY G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL G 132 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 151 Processing helix chain 'G' and resid 152 through 172 removed outlier: 4.134A pdb=" N LEU G 168 " --> pdb=" O TRP G 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS G 169 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER G 171 " --> pdb=" O SER G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 210 removed outlier: 4.246A pdb=" N ALA G 199 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 232 removed outlier: 3.616A pdb=" N TYR G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU G 222 " --> pdb=" O CYS G 218 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 224 " --> pdb=" O CYS G 220 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 225 " --> pdb=" O TYR G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 262 removed outlier: 4.863A pdb=" N VAL G 252 " --> pdb=" O ARG G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 274 removed outlier: 3.693A pdb=" N ASN G 268 " --> pdb=" O PHE G 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU G 272 " --> pdb=" O ASN G 268 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G 273 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 304 removed outlier: 3.729A pdb=" N PHE G 288 " --> pdb=" O GLY G 284 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 290 " --> pdb=" O TYR G 286 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE G 291 " --> pdb=" O PHE G 287 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Proline residue: G 301 - end of helix Processing helix chain 'G' and resid 308 through 316 removed outlier: 4.357A pdb=" N SER G 314 " --> pdb=" O ASN G 310 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 187 removed outlier: 9.374A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.886A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 62 removed outlier: 4.015A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 103 Processing sheet with id=AA5, first strand: chain 'C' and resid 121 through 125 removed outlier: 6.292A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.508A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.123A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.234A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.389A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 308 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.894A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 155 through 158 Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 190 360 hydrogen bonds defined for protein. 1023 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: 2.18 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1313 1.31 - 1.44: 2166 1.44 - 1.56: 4431 1.56 - 1.69: 3 1.69 - 1.82: 55 Bond restraints: 7968 Sorted by residual: bond pdb=" C TYR A 4 " pdb=" N PHA A 5 " ideal model delta sigma weight residual 1.329 1.515 -0.186 1.40e-02 5.10e+03 1.77e+02 bond pdb=" C LYS A 3 " pdb=" N TYR A 4 " ideal model delta sigma weight residual 1.329 1.506 -0.177 1.40e-02 5.10e+03 1.61e+02 bond pdb=" C DTR A 2 " pdb=" N LYS A 3 " ideal model delta sigma weight residual 1.329 1.491 -0.162 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP A 6 " pdb=" CD HYP A 6 " ideal model delta sigma weight residual 1.473 1.321 0.152 1.40e-02 5.10e+03 1.18e+02 bond pdb=" C PHA A 5 " pdb=" N HYP A 6 " ideal model delta sigma weight residual 1.329 1.477 -0.148 1.40e-02 5.10e+03 1.12e+02 ... (remaining 7963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 10628 2.47 - 4.94: 208 4.94 - 7.41: 54 7.41 - 9.88: 16 9.88 - 12.35: 3 Bond angle restraints: 10909 Sorted by residual: angle pdb=" N LYS B 46 " pdb=" CA LYS B 46 " pdb=" C LYS B 46 " ideal model delta sigma weight residual 111.71 101.84 9.87 1.15e+00 7.56e-01 7.37e+01 angle pdb=" C HIS G 143 " pdb=" N PRO G 144 " pdb=" CA PRO G 144 " ideal model delta sigma weight residual 120.45 113.00 7.45 1.11e+00 8.12e-01 4.50e+01 angle pdb=" N ASP C 186 " pdb=" CA ASP C 186 " pdb=" C ASP C 186 " ideal model delta sigma weight residual 108.63 118.39 -9.76 1.60e+00 3.91e-01 3.72e+01 angle pdb=" N ASP C 118 " pdb=" CA ASP C 118 " pdb=" C ASP C 118 " ideal model delta sigma weight residual 113.20 105.99 7.21 1.21e+00 6.83e-01 3.55e+01 angle pdb=" N LEU B 39 " pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " ideal model delta sigma weight residual 111.43 102.67 8.76 1.48e+00 4.57e-01 3.50e+01 ... (remaining 10904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4079 17.66 - 35.32: 411 35.32 - 52.97: 112 52.97 - 70.63: 13 70.63 - 88.29: 7 Dihedral angle restraints: 4622 sinusoidal: 1375 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 146.42 -53.42 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " pdb=" SG CYS C 114 " pdb=" CB CYS C 114 " ideal model delta sinusoidal sigma weight residual -86.00 -42.30 -43.70 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CB CYS G 112 " pdb=" SG CYS G 112 " pdb=" SG CYS G 186 " pdb=" CB CYS G 186 " ideal model delta sinusoidal sigma weight residual 93.00 127.92 -34.92 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 4619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1173 0.083 - 0.166: 111 0.166 - 0.249: 9 0.249 - 0.332: 3 0.332 - 0.414: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA ASP B 193 " pdb=" N ASP B 193 " pdb=" C ASP B 193 " pdb=" CB ASP B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CA SER B 44 " pdb=" N SER B 44 " pdb=" C SER B 44 " pdb=" CB SER B 44 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA ARG E 191 " pdb=" N ARG E 191 " pdb=" C ARG E 191 " pdb=" CB ARG E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1295 not shown) Planarity restraints: 1414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 150 " 0.060 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO E 151 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 179 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C GLN E 179 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN E 179 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG E 180 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 38 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C LEU B 38 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU B 38 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 1411 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2324 2.80 - 3.33: 7270 3.33 - 3.85: 13145 3.85 - 4.38: 14727 4.38 - 4.90: 25097 Nonbonded interactions: 62563 Sorted by model distance: nonbonded pdb=" O GLY E 112 " pdb=" OG SER E 184 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.279 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN G 81 " pdb=" OG SER G 160 " model vdw 2.342 3.120 nonbonded pdb=" O THR G 117 " pdb=" OG SER G 171 " model vdw 2.346 3.040 ... (remaining 62558 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: 0.820 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.090 Find NCS groups from input model: 0.080 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.186 7968 Z= 0.494 Angle : 0.930 12.354 10909 Z= 0.544 Chirality : 0.052 0.414 1298 Planarity : 0.005 0.090 1414 Dihedral : 16.041 88.290 2509 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 0.44 % Allowed : 29.22 % Favored : 70.34 % Cbeta Deviations : 0.10 % 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: -1.54 (0.25), residues: 1107 helix: 0.30 (0.30), residues: 326 sheet: -0.55 (0.36), residues: 227 loop : -2.10 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 211 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.001 PHE B 189 TYR 0.014 0.002 TYR C 111 ARG 0.011 0.001 ARG G 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.838 Fit side-chains REVERT: B 207 GLU cc_start: 0.7245 (tp30) cc_final: 0.5965 (pt0) REVERT: C 312 ASP cc_start: 0.7834 (t70) cc_final: 0.7555 (m-30) REVERT: E 75 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7222 (Cg_endo) REVERT: G 249 MET cc_start: 0.6359 (mmt) cc_final: 0.5994 (tpp) outliers start: 3 outliers final: 1 residues processed: 147 average time/residue: 0.1904 time to fit residues: 38.1767 Evaluate side-chains 127 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 261 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 333 GLN G 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 7968 Z= 0.234 Angle : 0.608 8.147 10909 Z= 0.315 Chirality : 0.042 0.149 1298 Planarity : 0.005 0.067 1414 Dihedral : 4.959 51.738 1183 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.11 % Allowed : 28.34 % Favored : 67.55 % 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: -1.32 (0.25), residues: 1107 helix: 0.58 (0.30), residues: 329 sheet: -0.69 (0.35), residues: 222 loop : -1.91 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 297 HIS 0.004 0.001 HIS E 35 PHE 0.008 0.001 PHE E 108 TYR 0.020 0.002 TYR E 190 ARG 0.003 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.843 Fit side-chains REVERT: B 46 LYS cc_start: 0.6824 (mtmm) cc_final: 0.6491 (mtpt) REVERT: B 207 GLU cc_start: 0.7106 (tp30) cc_final: 0.5972 (pt0) REVERT: B 216 GLU cc_start: 0.7961 (tt0) cc_final: 0.7633 (tt0) REVERT: C 52 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7494 (mtp85) REVERT: C 234 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: C 312 ASP cc_start: 0.7911 (t70) cc_final: 0.7468 (m-30) REVERT: E 140 MET cc_start: 0.2589 (mmt) cc_final: 0.2369 (mmp) REVERT: G 145 LEU cc_start: 0.5064 (pt) cc_final: 0.4848 (pt) REVERT: G 190 TRP cc_start: 0.6623 (OUTLIER) cc_final: 0.5258 (t-100) REVERT: G 304 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6047 (t80) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 0.1635 time to fit residues: 35.5273 Evaluate side-chains 135 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 190 TRP Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 83 optimal weight: 0.0270 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS C 220 GLN G 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7968 Z= 0.164 Angle : 0.596 16.526 10909 Z= 0.301 Chirality : 0.041 0.169 1298 Planarity : 0.004 0.061 1414 Dihedral : 4.706 47.247 1183 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.52 % Allowed : 29.22 % Favored : 67.25 % 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: -1.26 (0.25), residues: 1107 helix: 0.65 (0.30), residues: 336 sheet: -0.57 (0.35), residues: 223 loop : -1.94 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.019 0.001 PHE B 189 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.885 Fit side-chains REVERT: B 9 ASP cc_start: 0.7726 (m-30) cc_final: 0.7327 (m-30) REVERT: B 46 LYS cc_start: 0.6879 (mtmm) cc_final: 0.6582 (mtmt) REVERT: B 216 GLU cc_start: 0.7911 (tt0) cc_final: 0.7625 (tt0) REVERT: C 101 MET cc_start: 0.7890 (mtp) cc_final: 0.7641 (mtp) REVERT: C 234 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: C 312 ASP cc_start: 0.7841 (t70) cc_final: 0.7609 (m-30) REVERT: E 75 PRO cc_start: 0.7580 (Cg_exo) cc_final: 0.7271 (Cg_endo) REVERT: G 145 LEU cc_start: 0.5054 (pt) cc_final: 0.4844 (pt) REVERT: G 261 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6529 (t-100) outliers start: 24 outliers final: 9 residues processed: 157 average time/residue: 0.2058 time to fit residues: 45.4471 Evaluate side-chains 135 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 261 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.0370 chunk 60 optimal weight: 0.7980 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7968 Z= 0.250 Angle : 0.627 14.384 10909 Z= 0.320 Chirality : 0.043 0.219 1298 Planarity : 0.004 0.060 1414 Dihedral : 4.903 48.296 1183 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.02 % Allowed : 28.78 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.25), residues: 1107 helix: 0.64 (0.30), residues: 337 sheet: -0.76 (0.34), residues: 230 loop : -1.90 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 63 HIS 0.007 0.001 HIS E 35 PHE 0.012 0.001 PHE B 189 TYR 0.019 0.002 TYR E 50 ARG 0.004 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 0.790 Fit side-chains REVERT: B 25 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 46 LYS cc_start: 0.6798 (mtmm) cc_final: 0.6472 (mtmt) REVERT: C 234 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: C 312 ASP cc_start: 0.7804 (t70) cc_final: 0.7596 (m-30) REVERT: G 221 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: G 261 TRP cc_start: 0.6876 (OUTLIER) cc_final: 0.6246 (t-100) REVERT: G 304 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6231 (t80) outliers start: 41 outliers final: 26 residues processed: 156 average time/residue: 0.1683 time to fit residues: 36.5975 Evaluate side-chains 152 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 0.0020 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS G 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7968 Z= 0.169 Angle : 0.591 12.140 10909 Z= 0.297 Chirality : 0.041 0.176 1298 Planarity : 0.004 0.058 1414 Dihedral : 4.698 46.685 1183 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.99 % Allowed : 30.25 % Favored : 64.76 % 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: -1.26 (0.25), residues: 1107 helix: 0.79 (0.30), residues: 331 sheet: -0.72 (0.34), residues: 222 loop : -1.94 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 47 HIS 0.004 0.001 HIS B 213 PHE 0.009 0.001 PHE C 199 TYR 0.014 0.001 TYR E 190 ARG 0.003 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7666 (m-30) cc_final: 0.7277 (m-30) REVERT: B 25 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 46 LYS cc_start: 0.6808 (mtmm) cc_final: 0.6511 (mtmt) REVERT: B 216 GLU cc_start: 0.7751 (tt0) cc_final: 0.7538 (tt0) REVERT: C 52 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: C 234 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: G 261 TRP cc_start: 0.6665 (OUTLIER) cc_final: 0.6220 (t-100) outliers start: 34 outliers final: 22 residues processed: 157 average time/residue: 0.1923 time to fit residues: 42.3720 Evaluate side-chains 143 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 0.0060 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.0030 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7968 Z= 0.154 Angle : 0.572 11.066 10909 Z= 0.287 Chirality : 0.041 0.156 1298 Planarity : 0.004 0.056 1414 Dihedral : 4.546 48.437 1183 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.55 % Allowed : 30.98 % Favored : 64.46 % 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: -1.11 (0.26), residues: 1107 helix: 0.86 (0.30), residues: 337 sheet: -0.66 (0.33), residues: 247 loop : -1.88 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 47 HIS 0.004 0.001 HIS B 213 PHE 0.008 0.001 PHE C 199 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7642 (m-30) cc_final: 0.7242 (m-30) REVERT: B 216 GLU cc_start: 0.7716 (tt0) cc_final: 0.7504 (tt0) REVERT: C 234 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: C 327 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7302 (t) REVERT: E 75 PRO cc_start: 0.7577 (Cg_exo) cc_final: 0.7300 (Cg_endo) outliers start: 31 outliers final: 23 residues processed: 154 average time/residue: 0.1628 time to fit residues: 35.2178 Evaluate side-chains 149 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.0270 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.0070 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7968 Z= 0.174 Angle : 0.584 11.824 10909 Z= 0.294 Chirality : 0.041 0.156 1298 Planarity : 0.004 0.055 1414 Dihedral : 4.524 46.097 1183 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.70 % Allowed : 31.86 % Favored : 63.44 % 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: -1.07 (0.26), residues: 1107 helix: 0.87 (0.30), residues: 339 sheet: -0.59 (0.33), residues: 248 loop : -1.88 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE C 199 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.830 Fit side-chains REVERT: B 9 ASP cc_start: 0.7671 (m-30) cc_final: 0.7295 (m-30) REVERT: C 52 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: C 234 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: E 140 MET cc_start: 0.3125 (mmp) cc_final: 0.2735 (mmp) REVERT: G 304 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6099 (t80) outliers start: 32 outliers final: 24 residues processed: 148 average time/residue: 0.1764 time to fit residues: 36.0526 Evaluate side-chains 145 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 97 optimal weight: 0.0770 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.0870 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7968 Z= 0.163 Angle : 0.584 11.406 10909 Z= 0.292 Chirality : 0.041 0.158 1298 Planarity : 0.004 0.054 1414 Dihedral : 4.446 45.118 1183 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.26 % Allowed : 32.60 % Favored : 63.14 % 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: -1.07 (0.26), residues: 1107 helix: 0.85 (0.30), residues: 336 sheet: -0.50 (0.33), residues: 244 loop : -1.89 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.009 0.001 PHE C 199 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 ASP cc_start: 0.7687 (m-30) cc_final: 0.7300 (m-30) REVERT: C 63 TRP cc_start: 0.6970 (m100) cc_final: 0.6766 (m100) REVERT: C 234 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: C 327 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7260 (t) REVERT: E 140 MET cc_start: 0.3268 (mmp) cc_final: 0.3020 (mmp) outliers start: 29 outliers final: 24 residues processed: 142 average time/residue: 0.1650 time to fit residues: 33.5420 Evaluate side-chains 146 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7968 Z= 0.208 Angle : 0.602 12.083 10909 Z= 0.304 Chirality : 0.041 0.172 1298 Planarity : 0.004 0.053 1414 Dihedral : 4.559 46.481 1183 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.96 % Allowed : 32.75 % Favored : 63.29 % 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: -1.05 (0.26), residues: 1107 helix: 0.87 (0.30), residues: 334 sheet: -0.57 (0.34), residues: 234 loop : -1.81 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE E 239 TYR 0.012 0.001 TYR E 50 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.859 Fit side-chains REVERT: B 9 ASP cc_start: 0.7657 (m-30) cc_final: 0.7391 (m-30) REVERT: C 234 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: C 327 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7298 (t) REVERT: E 140 MET cc_start: 0.3320 (mmp) cc_final: 0.3120 (mmp) REVERT: G 304 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.6064 (t80) outliers start: 27 outliers final: 23 residues processed: 143 average time/residue: 0.1653 time to fit residues: 33.3769 Evaluate side-chains 145 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** G 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7968 Z= 0.293 Angle : 0.664 14.113 10909 Z= 0.340 Chirality : 0.043 0.224 1298 Planarity : 0.004 0.052 1414 Dihedral : 5.001 50.487 1183 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.70 % Allowed : 32.01 % Favored : 63.29 % 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: -1.23 (0.25), residues: 1107 helix: 0.67 (0.30), residues: 339 sheet: -0.64 (0.33), residues: 235 loop : -1.92 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS E 35 PHE 0.017 0.002 PHE E 239 TYR 0.019 0.002 TYR E 50 ARG 0.005 0.001 ARG E 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 0.758 Fit side-chains REVERT: B 216 GLU cc_start: 0.8012 (tt0) cc_final: 0.7727 (tt0) REVERT: C 52 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7736 (mtp85) REVERT: C 234 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: E 140 MET cc_start: 0.3424 (mmp) cc_final: 0.3208 (mmp) REVERT: G 221 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: G 304 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6063 (t80) outliers start: 32 outliers final: 24 residues processed: 149 average time/residue: 0.1730 time to fit residues: 35.7786 Evaluate side-chains 153 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 164 TRP Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 261 TRP Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 304 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 40.0000 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** G 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.190548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.145291 restraints weight = 11022.161| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.74 r_work: 0.3897 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7968 Z= 0.213 Angle : 0.632 14.542 10909 Z= 0.320 Chirality : 0.042 0.212 1298 Planarity : 0.004 0.053 1414 Dihedral : 4.844 50.660 1183 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.96 % Allowed : 33.77 % Favored : 62.26 % 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: -1.19 (0.25), residues: 1107 helix: 0.76 (0.30), residues: 339 sheet: -0.66 (0.34), residues: 227 loop : -1.90 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.025 0.001 PHE B 199 TYR 0.017 0.002 TYR C 85 ARG 0.003 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2064.47 seconds wall clock time: 37 minutes 20.59 seconds (2240.59 seconds total)