Starting phenix.real_space_refine on Fri Dec 8 12:20:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/12_2023/8grx_34216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/12_2023/8grx_34216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/12_2023/8grx_34216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/12_2023/8grx_34216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/12_2023/8grx_34216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/12_2023/8grx_34216.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.116 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 42 5.16 5 C 5256 2.51 5 N 1474 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 35": "OD1" <-> "OD2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8328 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1140 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3024 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1140 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "D" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3024 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.94, per 1000 atoms: 0.59 Number of scatterers: 8328 At special positions: 0 Unit cell: (124.063, 150.412, 77.9509, 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 42 16.00 O 1556 8.00 N 1474 7.00 C 5256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 245 " - pdb=" SG CYS B 296 " distance=2.02 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 245 " - pdb=" SG CYS D 296 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 396 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 22 sheets defined 27.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 3.953A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 54 through 82 Processing helix chain 'A' and resid 87 through 125 Processing helix chain 'A' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.953A pdb=" N LEU C 43 " --> pdb=" O TRP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 54 through 82 Processing helix chain 'C' and resid 87 through 125 Processing helix chain 'C' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET B 117 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP B 192 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG B 193 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU B 241 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU B 235 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 320 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 317 " --> pdb=" O LEU B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 268 Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL B 341 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET D 117 " --> pdb=" O TRP D 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 129 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP D 192 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG D 193 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU D 241 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU D 235 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN D 320 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET D 317 " --> pdb=" O LEU D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 268 Processing sheet with id=AC3, first strand: chain 'D' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL D 341 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 334 through 336 439 hydrogen bonds defined for protein. 1167 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: 2.66 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1926 1.33 - 1.45: 1864 1.45 - 1.57: 4692 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8550 Sorted by residual: bond pdb=" C HIS D 363 " pdb=" N PRO D 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C HIS B 363 " pdb=" N PRO B 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C GLY D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C GLY B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C PHE B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.46e+00 ... (remaining 8545 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.97: 382 106.97 - 114.13: 4586 114.13 - 121.30: 4788 121.30 - 128.46: 1728 128.46 - 135.63: 114 Bond angle restraints: 11598 Sorted by residual: angle pdb=" C GLU B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C GLU D 67 " pdb=" N PRO D 68 " pdb=" CA PRO D 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C ARG D 267 " pdb=" N PRO D 268 " pdb=" CA PRO D 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C ARG B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C GLY D 184 " pdb=" N PRO D 185 " pdb=" CA PRO D 185 " ideal model delta sigma weight residual 119.84 126.74 -6.90 1.25e+00 6.40e-01 3.05e+01 ... (remaining 11593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.18: 4966 25.18 - 50.36: 152 50.36 - 75.54: 18 75.54 - 100.72: 2 100.72 - 125.90: 4 Dihedral angle restraints: 5142 sinusoidal: 2098 harmonic: 3044 Sorted by residual: dihedral pdb=" CA GLN B 330 " pdb=" C GLN B 330 " pdb=" N PRO B 331 " pdb=" CA PRO B 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLN D 330 " pdb=" C GLN D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLY B 184 " pdb=" C GLY B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -67.33 -112.67 0 5.00e+00 4.00e-02 5.08e+02 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 758 0.040 - 0.080: 302 0.080 - 0.120: 116 0.120 - 0.159: 38 0.159 - 0.199: 2 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA SER A 54 " pdb=" N SER A 54 " pdb=" C SER A 54 " pdb=" CB SER A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA SER C 54 " pdb=" N SER C 54 " pdb=" C SER C 54 " pdb=" CB SER C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU D 235 " pdb=" CB LEU D 235 " pdb=" CD1 LEU D 235 " pdb=" CD2 LEU D 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1213 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 131 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 132 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 131 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 132 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ALA A 86 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 87 " -0.009 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2944 2.88 - 3.38: 7335 3.38 - 3.89: 14411 3.89 - 4.39: 16410 4.39 - 4.90: 26746 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" OG SER D 102 " pdb=" O GLY D 105 " model vdw 2.373 2.440 nonbonded pdb=" OG SER B 102 " pdb=" O GLY B 105 " model vdw 2.373 2.440 nonbonded pdb=" NE ARG B 253 " pdb=" O HIS B 300 " model vdw 2.522 2.520 nonbonded pdb=" NE ARG D 253 " pdb=" O HIS D 300 " model vdw 2.522 2.520 nonbonded pdb=" O ARG B 223 " pdb=" OH TYR B 251 " model vdw 2.551 2.440 ... (remaining 67841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.700 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: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.260 Find NCS groups from input model: 0.430 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.040 8550 Z= 0.429 Angle : 1.264 10.628 11598 Z= 0.795 Chirality : 0.051 0.199 1216 Planarity : 0.005 0.057 1514 Dihedral : 12.300 125.903 3170 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 8.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1040 helix: 1.26 (0.28), residues: 256 sheet: -0.08 (0.28), residues: 310 loop : -1.28 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 26 HIS 0.003 0.001 HIS D 209 PHE 0.010 0.002 PHE B 177 TYR 0.020 0.002 TYR B 197 ARG 0.005 0.001 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 1.3569 time to fit residues: 220.8633 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 58 GLN A 81 GLN A 117 GLN A 128 GLN A 140 HIS A 156 GLN B 92 HIS B 190 HIS B 205 GLN B 280 ASN B 290 HIS B 301 ASN B 346 GLN C 46 GLN C 58 GLN C 81 GLN C 117 GLN C 128 GLN C 140 HIS C 156 GLN D 92 HIS D 190 HIS D 205 GLN D 290 HIS D 301 ASN D 346 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8550 Z= 0.227 Angle : 0.568 7.191 11598 Z= 0.297 Chirality : 0.039 0.145 1216 Planarity : 0.006 0.092 1514 Dihedral : 5.602 89.213 1164 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.23 % Rotamer: Outliers : 2.24 % Allowed : 10.31 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 5.41 % 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: 1.33 (0.27), residues: 1040 helix: 3.58 (0.29), residues: 254 sheet: 0.35 (0.28), residues: 318 loop : -0.24 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 32 HIS 0.004 0.001 HIS D 92 PHE 0.009 0.001 PHE D 351 TYR 0.017 0.002 TYR B 372 ARG 0.004 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 1.2730 time to fit residues: 154.1854 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.2323 time to fit residues: 1.9403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN D 280 ASN ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8550 Z= 0.210 Angle : 0.518 6.548 11598 Z= 0.270 Chirality : 0.037 0.132 1216 Planarity : 0.006 0.097 1514 Dihedral : 5.057 81.524 1164 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 2.24 % Allowed : 11.88 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.71 (0.27), residues: 1040 helix: 3.79 (0.29), residues: 254 sheet: 0.73 (0.29), residues: 316 loop : -0.05 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 32 HIS 0.002 0.001 HIS A 140 PHE 0.006 0.001 PHE D 351 TYR 0.012 0.001 TYR D 197 ARG 0.003 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 1.1686 time to fit residues: 137.6507 Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.3157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 27 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8550 Z= 0.210 Angle : 0.499 6.379 11598 Z= 0.259 Chirality : 0.037 0.128 1216 Planarity : 0.006 0.100 1514 Dihedral : 4.923 77.202 1164 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.54 % Favored : 98.27 % Rotamer: Outliers : 3.36 % Allowed : 11.21 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.71 (0.27), residues: 1040 helix: 3.75 (0.29), residues: 254 sheet: 0.64 (0.28), residues: 332 loop : 0.04 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 32 HIS 0.004 0.001 HIS B 363 PHE 0.005 0.001 PHE B 351 TYR 0.011 0.001 TYR B 197 ARG 0.004 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 116 average time/residue: 1.0518 time to fit residues: 131.5116 Evaluate side-chains 114 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.7812 time to fit residues: 6.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 405 HIS C 46 GLN D 405 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8550 Z= 0.300 Angle : 0.539 6.734 11598 Z= 0.278 Chirality : 0.039 0.136 1216 Planarity : 0.006 0.106 1514 Dihedral : 5.029 75.047 1164 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.50 % Favored : 97.31 % Rotamer: Outliers : 3.81 % Allowed : 11.43 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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 (0.27), residues: 1040 helix: 3.45 (0.29), residues: 254 sheet: 0.60 (0.28), residues: 334 loop : 0.04 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 32 HIS 0.003 0.001 HIS A 140 PHE 0.005 0.001 PHE D 351 TYR 0.013 0.002 TYR B 197 ARG 0.005 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 117 average time/residue: 1.1273 time to fit residues: 141.3024 Evaluate side-chains 112 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.7212 time to fit residues: 6.0650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8550 Z= 0.221 Angle : 0.505 6.519 11598 Z= 0.260 Chirality : 0.037 0.135 1216 Planarity : 0.006 0.114 1514 Dihedral : 4.876 72.617 1164 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.69 % Allowed : 12.78 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.72 (0.27), residues: 1040 helix: 3.62 (0.29), residues: 254 sheet: 0.59 (0.28), residues: 336 loop : 0.18 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 32 HIS 0.004 0.001 HIS B 363 PHE 0.003 0.001 PHE D 381 TYR 0.011 0.001 TYR D 197 ARG 0.004 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 108 average time/residue: 1.0509 time to fit residues: 122.2742 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS C 46 GLN D 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8550 Z= 0.214 Angle : 0.499 5.969 11598 Z= 0.257 Chirality : 0.037 0.135 1216 Planarity : 0.006 0.110 1514 Dihedral : 4.807 70.165 1164 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 13.68 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.27), residues: 1040 helix: 3.63 (0.29), residues: 254 sheet: 0.64 (0.28), residues: 336 loop : 0.30 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 32 HIS 0.005 0.001 HIS B 363 PHE 0.004 0.001 PHE B 381 TYR 0.011 0.001 TYR B 197 ARG 0.005 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 100 average time/residue: 1.0842 time to fit residues: 116.8862 Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 1.3150 time to fit residues: 4.1797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN B 363 HIS D 147 GLN D 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8550 Z= 0.182 Angle : 0.476 5.670 11598 Z= 0.247 Chirality : 0.036 0.132 1216 Planarity : 0.006 0.105 1514 Dihedral : 4.734 69.228 1164 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 13.68 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.95 (0.27), residues: 1040 helix: 3.71 (0.29), residues: 254 sheet: 0.69 (0.28), residues: 340 loop : 0.43 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 32 HIS 0.005 0.001 HIS B 363 PHE 0.004 0.001 PHE C 33 TYR 0.011 0.001 TYR D 377 ARG 0.012 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 1.2525 time to fit residues: 138.1293 Evaluate side-chains 93 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 61 optimal weight: 0.1980 chunk 98 optimal weight: 0.0170 chunk 60 optimal weight: 0.5980 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 314 ASN B 363 HIS C 46 GLN D 314 ASN D 363 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8550 Z= 0.131 Angle : 0.461 5.211 11598 Z= 0.238 Chirality : 0.035 0.129 1216 Planarity : 0.005 0.103 1514 Dihedral : 4.525 66.477 1164 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.24 % Allowed : 15.58 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 2.25 (0.27), residues: 1040 helix: 3.98 (0.29), residues: 254 sheet: 0.93 (0.28), residues: 336 loop : 0.53 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 32 HIS 0.005 0.001 HIS B 363 PHE 0.006 0.001 PHE D 354 TYR 0.012 0.001 TYR B 377 ARG 0.002 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 1.1678 time to fit residues: 130.8007 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.3003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0020 chunk 68 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 chunk 65 optimal weight: 0.0060 chunk 87 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS C 46 GLN D 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8550 Z= 0.140 Angle : 0.463 6.143 11598 Z= 0.239 Chirality : 0.035 0.132 1216 Planarity : 0.005 0.102 1514 Dihedral : 4.473 64.696 1164 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 16.82 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 2.34 (0.27), residues: 1040 helix: 3.95 (0.28), residues: 254 sheet: 1.04 (0.28), residues: 340 loop : 0.60 (0.33), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 32 HIS 0.005 0.001 HIS D 363 PHE 0.005 0.001 PHE C 33 TYR 0.012 0.001 TYR B 377 ARG 0.007 0.000 ARG C 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 97 average time/residue: 1.0823 time to fit residues: 112.8978 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.3440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS D 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.194494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143608 restraints weight = 9046.855| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.62 r_work: 0.3326 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8550 Z= 0.218 Angle : 0.498 7.232 11598 Z= 0.256 Chirality : 0.037 0.140 1216 Planarity : 0.005 0.101 1514 Dihedral : 4.597 64.923 1164 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.02 % Allowed : 16.70 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 2.19 (0.27), residues: 1040 helix: 3.85 (0.28), residues: 254 sheet: 1.02 (0.29), residues: 332 loop : 0.44 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 32 HIS 0.005 0.001 HIS D 363 PHE 0.005 0.001 PHE D 381 TYR 0.012 0.001 TYR B 377 ARG 0.007 0.000 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.87 seconds wall clock time: 56 minutes 48.14 seconds (3408.14 seconds total)